Starting phenix.real_space_refine on Sat Mar 7 12:57:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qum_4640/03_2026/6qum_4640_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qum_4640/03_2026/6qum_4640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6qum_4640/03_2026/6qum_4640_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qum_4640/03_2026/6qum_4640_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qum_4640/03_2026/6qum_4640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qum_4640/03_2026/6qum_4640.map" } resolution = 3.25 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= 0.004 sd= 0.023 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 4 5.49 5 Mg 1 5.21 5 S 128 5.16 5 C 28654 2.51 5 N 7834 2.21 5 O 8279 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 142 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44900 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 4477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4477 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4477 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4477 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3682 Classifications: {'peptide': 469} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 442} Chain: "F" Number of atoms: 3686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3686 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 443} Chain: "G" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1628 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 808 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1437 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 7, 'TRANS': 178} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 788 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1441 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 7, 'TRANS': 179} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "M" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2514 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 12, 'TRANS': 307} Chain: "N" Number of atoms: 4858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 4858 Classifications: {'peptide': 649} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 36, 'TRANS': 612} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'HIS:plan': 3, 'ASP:plan': 3, 'PHE:plan': 2, 'ARG:plan': 6, 'GLU:plan': 9, 'TYR:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 120 Chain: "O" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "P" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "Q" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "R" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "S" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "T" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "U" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "V" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "W" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "X" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 504 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "Y" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "Z" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 55 Unusual residues: {' MG': 1, 'ADP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 9.09, per 1000 atoms: 0.20 Number of scatterers: 44900 At special positions: 0 Unit cell: (149.73, 151.9, 254.975, 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 128 16.00 P 4 15.00 Mg 1 11.99 O 8279 8.00 N 7834 7.00 C 28654 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS M 267 " - pdb=" SG CYS M 322 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.69 Conformation dependent library (CDL) restraints added in 1.8 seconds 11644 Ramachandran restraints generated. 5822 Oldfield, 0 Emsley, 5822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10590 Finding SS restraints... Secondary structure from input PDB file: 202 helices and 40 sheets defined 56.4% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 90 through 98 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 259 through 269 removed outlier: 4.322A pdb=" N VAL A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 298 through 315 removed outlier: 3.710A pdb=" N GLY A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 341 removed outlier: 3.687A pdb=" N TRP A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 395 through 403 removed outlier: 4.762A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.970A pdb=" N ARG A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 471 removed outlier: 4.665A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 494 Processing helix chain 'A' and resid 508 through 532 removed outlier: 3.604A pdb=" N ARG A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 removed outlier: 4.114A pdb=" N ARG A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 577 removed outlier: 4.255A pdb=" N GLU A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 removed outlier: 3.610A pdb=" N GLY B 99 " --> pdb=" O ARG B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 268 through 272 removed outlier: 3.731A pdb=" N GLU B 271 " --> pdb=" O GLU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 283 removed outlier: 3.596A pdb=" N HIS B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 280 through 283' Processing helix chain 'B' and resid 295 through 316 removed outlier: 5.854A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN B 316 " --> pdb=" O TYR B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.640A pdb=" N TRP B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 393 through 403 Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.886A pdb=" N ALA B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 433 No H-bonds generated for 'chain 'B' and resid 431 through 433' Processing helix chain 'B' and resid 435 through 443 Processing helix chain 'B' and resid 446 through 464 removed outlier: 3.737A pdb=" N ALA B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 471 removed outlier: 3.700A pdb=" N VAL B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.666A pdb=" N LEU B 476 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 494 Processing helix chain 'B' and resid 508 through 533 removed outlier: 4.496A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 541 removed outlier: 4.096A pdb=" N ILE B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN B 541 " --> pdb=" O ASP B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 550 Processing helix chain 'B' and resid 558 through 561 Processing helix chain 'B' and resid 562 through 576 removed outlier: 3.511A pdb=" N GLN B 571 " --> pdb=" O MET B 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 Processing helix chain 'C' and resid 235 through 244 Processing helix chain 'C' and resid 258 through 269 removed outlier: 4.140A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 297 through 315 removed outlier: 4.285A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE C 303 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 341 removed outlier: 3.590A pdb=" N TRP C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 393 through 401 removed outlier: 3.956A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 446 through 472 removed outlier: 4.335A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 494 removed outlier: 3.673A pdb=" N ILE C 484 " --> pdb=" O GLU C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 528 removed outlier: 3.600A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 540 removed outlier: 3.529A pdb=" N ILE C 539 " --> pdb=" O SER C 535 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU C 540 " --> pdb=" O ILE C 536 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 535 through 540' Processing helix chain 'C' and resid 543 through 550 removed outlier: 3.891A pdb=" N ARG C 547 " --> pdb=" O PRO C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 554 removed outlier: 3.853A pdb=" N VAL C 554 " --> pdb=" O ALA C 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 551 through 554' Processing helix chain 'C' and resid 558 through 573 removed outlier: 3.751A pdb=" N GLU C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 removed outlier: 4.014A pdb=" N ARG D 124 " --> pdb=" O PRO D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.791A pdb=" N ILE D 163 " --> pdb=" O PRO D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 178 removed outlier: 3.529A pdb=" N LEU D 177 " --> pdb=" O ARG D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 211 removed outlier: 3.962A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 249 removed outlier: 3.513A pdb=" N ARG D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.631A pdb=" N TYR D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 296 removed outlier: 4.287A pdb=" N ILE D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 340 through 347 removed outlier: 3.561A pdb=" N HIS D 344 " --> pdb=" O SER D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 396 removed outlier: 4.247A pdb=" N ASP D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE D 392 " --> pdb=" O ASN D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 422 removed outlier: 3.757A pdb=" N ARG D 409 " --> pdb=" O THR D 405 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG D 420 " --> pdb=" O ASP D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'D' and resid 466 through 471 removed outlier: 3.968A pdb=" N ILE D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TRP D 471 " --> pdb=" O LEU D 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 466 through 471' Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.956A pdb=" N MET E 88 " --> pdb=" O SER E 85 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 85 through 89' Processing helix chain 'E' and resid 135 through 141 Processing helix chain 'E' and resid 160 through 168 Processing helix chain 'E' and resid 175 through 178 Processing helix chain 'E' and resid 197 through 211 removed outlier: 4.451A pdb=" N THR E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 215 removed outlier: 3.912A pdb=" N SER E 215 " --> pdb=" O GLY E 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 212 through 215' Processing helix chain 'E' and resid 227 through 249 removed outlier: 3.781A pdb=" N ARG E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.821A pdb=" N HIS E 249 " --> pdb=" O LEU E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 272 removed outlier: 3.901A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.836A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 331 Processing helix chain 'E' and resid 340 through 345 removed outlier: 3.668A pdb=" N HIS E 344 " --> pdb=" O SER E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 397 Processing helix chain 'E' and resid 405 through 422 removed outlier: 3.714A pdb=" N ARG E 409 " --> pdb=" O THR E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 455 through 462 Processing helix chain 'E' and resid 466 through 471 Processing helix chain 'F' and resid 135 through 141 Processing helix chain 'F' and resid 159 through 171 removed outlier: 3.537A pdb=" N ILE F 163 " --> pdb=" O PRO F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 179 Processing helix chain 'F' and resid 198 through 212 Processing helix chain 'F' and resid 233 through 248 removed outlier: 3.625A pdb=" N VAL F 241 " --> pdb=" O MET F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 273 removed outlier: 3.884A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 340 through 345 Processing helix chain 'F' and resid 361 through 365 Processing helix chain 'F' and resid 374 through 400 removed outlier: 3.902A pdb=" N LYS F 394 " --> pdb=" O VAL F 390 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU F 395 " --> pdb=" O ASP F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 422 removed outlier: 3.756A pdb=" N ASP F 416 " --> pdb=" O LEU F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 455 through 462 Processing helix chain 'G' and resid 7 through 71 removed outlier: 3.718A pdb=" N LEU G 11 " --> pdb=" O THR G 7 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP G 26 " --> pdb=" O GLN G 22 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA G 37 " --> pdb=" O ASP G 33 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU G 45 " --> pdb=" O GLY G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 Processing helix chain 'G' and resid 122 through 169 removed outlier: 4.185A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 209 removed outlier: 3.628A pdb=" N LYS G 195 " --> pdb=" O THR G 191 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG G 204 " --> pdb=" O LYS G 200 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU G 205 " --> pdb=" O ILE G 201 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA G 206 " --> pdb=" O GLU G 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 16 removed outlier: 3.710A pdb=" N PHE H 13 " --> pdb=" O THR H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 39 Processing helix chain 'H' and resid 56 through 62 Processing helix chain 'H' and resid 76 through 80 removed outlier: 3.543A pdb=" N GLU H 79 " --> pdb=" O GLY H 76 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA H 80 " --> pdb=" O LEU H 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 76 through 80' Processing helix chain 'H' and resid 85 through 99 Processing helix chain 'I' and resid 19 through 104 removed outlier: 3.770A pdb=" N GLU I 45 " --> pdb=" O LYS I 41 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS I 102 " --> pdb=" O ALA I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 119 removed outlier: 3.751A pdb=" N ALA I 110 " --> pdb=" O ARG I 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 94 removed outlier: 3.968A pdb=" N GLU J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA J 34 " --> pdb=" O VAL J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 115 removed outlier: 3.896A pdb=" N ARG J 105 " --> pdb=" O PRO J 101 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU J 107 " --> pdb=" O VAL J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 135 removed outlier: 3.614A pdb=" N LEU J 131 " --> pdb=" O ASP J 127 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 159 No H-bonds generated for 'chain 'J' and resid 157 through 159' Processing helix chain 'J' and resid 166 through 187 removed outlier: 5.176A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 107 removed outlier: 3.894A pdb=" N ARG K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 119 removed outlier: 4.144A pdb=" N ALA K 112 " --> pdb=" O ASP K 108 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU K 113 " --> pdb=" O GLU K 109 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU K 119 " --> pdb=" O LEU K 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 91 removed outlier: 5.502A pdb=" N GLN L 43 " --> pdb=" O LYS L 39 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU L 46 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU L 78 " --> pdb=" O GLN L 74 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL L 79 " --> pdb=" O ALA L 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 128 through 130 No H-bonds generated for 'chain 'L' and resid 128 through 130' Processing helix chain 'L' and resid 131 through 136 Processing helix chain 'L' and resid 166 through 188 removed outlier: 5.278A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN L 184 " --> pdb=" O SER L 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 18 removed outlier: 3.924A pdb=" N LEU M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG M 11 " --> pdb=" O TYR M 7 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR M 18 " --> pdb=" O VAL M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 28 removed outlier: 4.327A pdb=" N PHE M 25 " --> pdb=" O LYS M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 33 through 41 Processing helix chain 'M' and resid 43 through 48 removed outlier: 3.628A pdb=" N GLY M 47 " --> pdb=" O VAL M 44 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU M 48 " --> pdb=" O TYR M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 69 Processing helix chain 'M' and resid 78 through 85 Processing helix chain 'M' and resid 89 through 106 Processing helix chain 'M' and resid 120 through 127 removed outlier: 3.978A pdb=" N TRP M 124 " --> pdb=" O ARG M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 141 Processing helix chain 'M' and resid 145 through 151 removed outlier: 3.528A pdb=" N ARG M 149 " --> pdb=" O HIS M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 182 Processing helix chain 'M' and resid 188 through 207 Processing helix chain 'M' and resid 213 through 217 removed outlier: 3.727A pdb=" N ALA M 216 " --> pdb=" O ALA M 213 " (cutoff:3.500A) Processing helix chain 'M' and resid 226 through 235 Processing helix chain 'M' and resid 238 through 244 Processing helix chain 'M' and resid 257 through 274 Processing helix chain 'M' and resid 275 through 279 Processing helix chain 'M' and resid 283 through 310 removed outlier: 3.827A pdb=" N GLU M 292 " --> pdb=" O ALA M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 312 through 320 removed outlier: 4.437A pdb=" N GLU M 317 " --> pdb=" O ALA M 314 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLU M 318 " --> pdb=" O GLN M 315 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL M 320 " --> pdb=" O GLU M 317 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 27 removed outlier: 3.871A pdb=" N ALA N 27 " --> pdb=" O SER N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 71 Processing helix chain 'N' and resid 83 through 117 Proline residue: N 93 - end of helix removed outlier: 3.811A pdb=" N GLN N 106 " --> pdb=" O THR N 102 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA N 117 " --> pdb=" O ALA N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 119 through 129 Processing helix chain 'N' and resid 149 through 160 removed outlier: 3.661A pdb=" N VAL N 153 " --> pdb=" O GLU N 149 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ALA N 156 " --> pdb=" O LEU N 152 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU N 157 " --> pdb=" O VAL N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 184 through 197 Processing helix chain 'N' and resid 207 through 211 removed outlier: 3.795A pdb=" N GLU N 210 " --> pdb=" O ALA N 207 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU N 211 " --> pdb=" O LEU N 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 207 through 211' Processing helix chain 'N' and resid 212 through 244 Proline residue: N 228 - end of helix Processing helix chain 'N' and resid 245 through 267 removed outlier: 3.860A pdb=" N GLU N 267 " --> pdb=" O LEU N 263 " (cutoff:3.500A) Processing helix chain 'N' and resid 283 through 285 No H-bonds generated for 'chain 'N' and resid 283 through 285' Processing helix chain 'N' and resid 286 through 294 Processing helix chain 'N' and resid 327 through 329 No H-bonds generated for 'chain 'N' and resid 327 through 329' Processing helix chain 'N' and resid 330 through 335 Processing helix chain 'N' and resid 349 through 363 Proline residue: N 356 - end of helix removed outlier: 3.609A pdb=" N MET N 361 " --> pdb=" O PHE N 357 " (cutoff:3.500A) Processing helix chain 'N' and resid 365 through 385 Processing helix chain 'N' and resid 399 through 425 removed outlier: 3.550A pdb=" N ILE N 403 " --> pdb=" O LYS N 399 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TRP N 416 " --> pdb=" O TRP N 412 " (cutoff:3.500A) Processing helix chain 'N' and resid 459 through 489 removed outlier: 3.726A pdb=" N GLY N 471 " --> pdb=" O SER N 467 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS N 489 " --> pdb=" O LEU N 485 " (cutoff:3.500A) Processing helix chain 'N' and resid 491 through 516 removed outlier: 4.094A pdb=" N PHE N 495 " --> pdb=" O HIS N 491 " (cutoff:3.500A) Processing helix chain 'N' and resid 523 through 541 removed outlier: 4.167A pdb=" N LEU N 527 " --> pdb=" O TRP N 523 " (cutoff:3.500A) Processing helix chain 'N' and resid 549 through 560 removed outlier: 3.973A pdb=" N THR N 553 " --> pdb=" O PRO N 549 " (cutoff:3.500A) Processing helix chain 'N' and resid 562 through 588 Processing helix chain 'N' and resid 593 through 613 Processing helix chain 'N' and resid 614 through 627 Proline residue: N 620 - end of helix Processing helix chain 'N' and resid 627 through 632 removed outlier: 3.886A pdb=" N PHE N 632 " --> pdb=" O PHE N 628 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 48 removed outlier: 4.343A pdb=" N GLY O 13 " --> pdb=" O GLY O 9 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU O 14 " --> pdb=" O LEU O 10 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG O 36 " --> pdb=" O VAL O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 61 Processing helix chain 'O' and resid 63 through 80 Processing helix chain 'P' and resid 10 through 48 removed outlier: 3.569A pdb=" N LEU P 14 " --> pdb=" O LEU P 10 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG P 36 " --> pdb=" O VAL P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 61 removed outlier: 3.564A pdb=" N ALA P 55 " --> pdb=" O ASN P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 79 Processing helix chain 'Q' and resid 10 through 48 removed outlier: 3.905A pdb=" N ALA Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG Q 36 " --> pdb=" O VAL Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 61 Processing helix chain 'Q' and resid 63 through 79 Processing helix chain 'R' and resid 10 through 48 removed outlier: 4.011A pdb=" N LEU R 14 " --> pdb=" O LEU R 10 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG R 36 " --> pdb=" O VAL R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 61 removed outlier: 3.868A pdb=" N LEU R 56 " --> pdb=" O PHE R 52 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ILE R 57 " --> pdb=" O GLY R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 80 Processing helix chain 'S' and resid 11 through 48 removed outlier: 4.061A pdb=" N ARG S 36 " --> pdb=" O VAL S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 61 Processing helix chain 'S' and resid 63 through 80 Processing helix chain 'T' and resid 10 through 48 removed outlier: 4.068A pdb=" N ILE T 15 " --> pdb=" O ASP T 11 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ALA T 16 " --> pdb=" O ARG T 12 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL T 17 " --> pdb=" O GLY T 13 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU T 25 " --> pdb=" O LEU T 21 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG T 36 " --> pdb=" O VAL T 32 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE T 37 " --> pdb=" O ALA T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 61 removed outlier: 3.563A pdb=" N ALA T 55 " --> pdb=" O ASN T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 63 through 80 Processing helix chain 'U' and resid 10 through 48 removed outlier: 3.940A pdb=" N LEU U 14 " --> pdb=" O LEU U 10 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG U 36 " --> pdb=" O VAL U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 61 Processing helix chain 'U' and resid 62 through 80 removed outlier: 4.114A pdb=" N VAL U 66 " --> pdb=" O PRO U 62 " (cutoff:3.500A) Processing helix chain 'V' and resid 10 through 48 removed outlier: 3.555A pdb=" N LEU V 14 " --> pdb=" O LEU V 10 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG V 36 " --> pdb=" O VAL V 32 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE V 37 " --> pdb=" O ALA V 33 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 61 Processing helix chain 'V' and resid 63 through 79 Processing helix chain 'W' and resid 11 through 48 removed outlier: 4.071A pdb=" N ARG W 36 " --> pdb=" O VAL W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 51 through 61 Processing helix chain 'W' and resid 62 through 80 removed outlier: 4.278A pdb=" N VAL W 66 " --> pdb=" O PRO W 62 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 48 removed outlier: 3.910A pdb=" N ARG X 36 " --> pdb=" O VAL X 32 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 61 Processing helix chain 'X' and resid 63 through 80 removed outlier: 3.566A pdb=" N LEU X 80 " --> pdb=" O LEU X 76 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 46 removed outlier: 4.042A pdb=" N ARG Y 36 " --> pdb=" O VAL Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 52 through 61 removed outlier: 4.938A pdb=" N PHE Y 58 " --> pdb=" O THR Y 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 63 through 79 removed outlier: 4.060A pdb=" N ILE Y 67 " --> pdb=" O GLU Y 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 48 removed outlier: 3.860A pdb=" N GLY Z 13 " --> pdb=" O GLY Z 9 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA Z 16 " --> pdb=" O ARG Z 12 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL Z 17 " --> pdb=" O GLY Z 13 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA Z 22 " --> pdb=" O GLY Z 18 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG Z 36 " --> pdb=" O VAL Z 32 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP Z 48 " --> pdb=" O ALA Z 44 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 60 removed outlier: 3.990A pdb=" N ILE Z 57 " --> pdb=" O GLY Z 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 80 removed outlier: 3.539A pdb=" N LEU Z 80 " --> pdb=" O LEU Z 76 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.984A pdb=" N ILE F 11 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLU F 22 " --> pdb=" O ILE F 11 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR F 13 " --> pdb=" O PHE F 20 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TYR F 54 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL F 50 " --> pdb=" O TYR F 54 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL F 56 " --> pdb=" O ILE F 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 3 through 9 current: chain 'F' and resid 72 through 76 removed outlier: 3.534A pdb=" N LEU F 75 " --> pdb=" O LYS F 6 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LYS F 6 " --> pdb=" O LEU F 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.984A pdb=" N ILE F 11 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLU F 22 " --> pdb=" O ILE F 11 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR F 13 " --> pdb=" O PHE F 20 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TYR F 54 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL F 50 " --> pdb=" O TYR F 54 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL F 56 " --> pdb=" O ILE F 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 42 through 51 current: chain 'A' and resid 27 through 30 removed outlier: 3.553A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 3 through 9 current: chain 'F' and resid 72 through 76 removed outlier: 3.534A pdb=" N LEU F 75 " --> pdb=" O LYS F 6 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LYS F 6 " --> pdb=" O LEU F 75 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 84 removed outlier: 6.683A pdb=" N GLY A 82 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ALA A 289 " --> pdb=" O GLY A 82 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TYR A 84 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N THR A 291 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL A 249 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYS A 255 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 82 through 84 removed outlier: 6.683A pdb=" N GLY A 82 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ALA A 289 " --> pdb=" O GLY A 82 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TYR A 84 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N THR A 291 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL A 249 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYS A 255 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA A 224 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL A 384 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE A 226 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 143 through 148 removed outlier: 6.620A pdb=" N PHE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ALA A 118 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 128 through 129 removed outlier: 3.548A pdb=" N VAL A 173 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 50 through 51 removed outlier: 5.199A pdb=" N ILE B 6 " --> pdb=" O LYS B 17 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LYS B 17 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 50 through 51 removed outlier: 6.523A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AB2, first strand: chain 'B' and resid 82 through 84 removed outlier: 6.404A pdb=" N GLY B 82 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ALA B 289 " --> pdb=" O GLY B 82 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TYR B 84 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N THR B 291 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS B 255 " --> pdb=" O ASP B 325 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG B 197 " --> pdb=" O ILE B 369 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 116 through 118 Processing sheet with id=AB4, first strand: chain 'B' and resid 120 through 121 removed outlier: 3.767A pdb=" N GLY B 136 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 128 through 129 removed outlier: 3.611A pdb=" N VAL B 173 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 383 through 384 removed outlier: 7.434A pdb=" N VAL B 384 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE B 226 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 2 through 10 removed outlier: 6.639A pdb=" N ILE C 15 " --> pdb=" O GLN C 7 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ILE C 9 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA C 13 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE C 39 " --> pdb=" O ASP C 26 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP C 26 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE C 27 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE C 2 " --> pdb=" O SER C 66 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB9, first strand: chain 'C' and resid 82 through 84 removed outlier: 6.355A pdb=" N GLY C 82 " --> pdb=" O LEU C 287 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ALA C 289 " --> pdb=" O GLY C 82 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N TYR C 84 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C 251 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ASP C 325 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL C 253 " --> pdb=" O ASP C 325 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG C 197 " --> pdb=" O ILE C 369 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 82 through 84 removed outlier: 6.355A pdb=" N GLY C 82 " --> pdb=" O LEU C 287 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ALA C 289 " --> pdb=" O GLY C 82 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N TYR C 84 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C 251 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ASP C 325 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL C 253 " --> pdb=" O ASP C 325 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA C 224 " --> pdb=" O GLY C 382 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 117 through 118 Processing sheet with id=AC3, first strand: chain 'C' and resid 120 through 121 removed outlier: 6.962A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 128 through 129 removed outlier: 3.531A pdb=" N VAL C 173 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 11 through 15 removed outlier: 6.003A pdb=" N ILE D 11 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLU D 22 " --> pdb=" O ILE D 11 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N TYR D 13 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE D 32 " --> pdb=" O VAL D 76 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 81 through 84 Processing sheet with id=AC7, first strand: chain 'D' and resid 92 through 93 removed outlier: 5.805A pdb=" N PHE D 93 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL D 253 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILE D 311 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL D 255 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE D 313 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU D 257 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N SER D 315 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE D 152 " --> pdb=" O LEU D 314 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 5 through 8 removed outlier: 5.782A pdb=" N LEU J 121 " --> pdb=" O GLN J 143 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 81 through 84 Processing sheet with id=AD1, first strand: chain 'E' and resid 131 through 132 Processing sheet with id=AD2, first strand: chain 'E' and resid 217 through 219 removed outlier: 3.513A pdb=" N VAL E 308 " --> pdb=" O GLY E 299 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 217 through 219 removed outlier: 5.856A pdb=" N ILE E 152 " --> pdb=" O LEU E 314 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 81 through 84 Processing sheet with id=AD5, first strand: chain 'F' and resid 92 through 93 removed outlier: 6.192A pdb=" N PHE F 93 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LYS F 223 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL F 253 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ILE F 311 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL F 255 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE F 313 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU F 257 " --> pdb=" O ILE F 313 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N SER F 315 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE F 152 " --> pdb=" O LEU F 314 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 124 through 125 removed outlier: 4.779A pdb=" N VAL F 300 " --> pdb=" O ARG F 125 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AD8, first strand: chain 'G' and resid 90 through 96 Processing sheet with id=AD9, first strand: chain 'H' and resid 2 through 4 Processing sheet with id=AE1, first strand: chain 'N' and resid 31 through 32 Processing sheet with id=AE2, first strand: chain 'N' and resid 31 through 32 Processing sheet with id=AE3, first strand: chain 'N' and resid 140 through 145 Processing sheet with id=AE4, first strand: chain 'N' and resid 389 through 391 2749 hydrogen bonds defined for protein. 8004 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: 10.20 Time building geometry restraints manager: 4.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 7725 1.32 - 1.44: 11005 1.44 - 1.57: 26688 1.57 - 1.69: 8 1.69 - 1.81: 242 Bond restraints: 45668 Sorted by residual: bond pdb=" C PHE B 559 " pdb=" N PRO B 560 " ideal model delta sigma weight residual 1.334 1.383 -0.049 8.40e-03 1.42e+04 3.41e+01 bond pdb=" CG LEU O 60 " pdb=" CD1 LEU O 60 " ideal model delta sigma weight residual 1.521 1.406 0.115 3.30e-02 9.18e+02 1.21e+01 bond pdb=" C LYS L 39 " pdb=" O LYS L 39 " ideal model delta sigma weight residual 1.234 1.194 0.040 1.40e-02 5.10e+03 8.03e+00 bond pdb=" CB VAL A 218 " pdb=" CG2 VAL A 218 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.70e+00 bond pdb=" C LYS L 39 " pdb=" N ALA L 40 " ideal model delta sigma weight residual 1.332 1.300 0.033 1.40e-02 5.10e+03 5.46e+00 ... (remaining 45663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 60814 3.51 - 7.02: 874 7.02 - 10.53: 122 10.53 - 14.04: 22 14.04 - 17.55: 5 Bond angle restraints: 61837 Sorted by residual: angle pdb=" N GLY A 366 " pdb=" CA GLY A 366 " pdb=" C GLY A 366 " ideal model delta sigma weight residual 113.18 126.56 -13.38 2.37e+00 1.78e-01 3.19e+01 angle pdb=" C TRP N 545 " pdb=" N LEU N 546 " pdb=" CA LEU N 546 " ideal model delta sigma weight residual 122.74 130.77 -8.03 1.44e+00 4.82e-01 3.11e+01 angle pdb=" C GLU F 406 " pdb=" N ASN F 407 " pdb=" CA ASN F 407 " ideal model delta sigma weight residual 121.54 132.01 -10.47 1.91e+00 2.74e-01 3.00e+01 angle pdb=" N THR N 348 " pdb=" CA THR N 348 " pdb=" C THR N 348 " ideal model delta sigma weight residual 109.81 121.50 -11.69 2.21e+00 2.05e-01 2.80e+01 angle pdb=" C ASP F 318 " pdb=" N ASP F 319 " pdb=" CA ASP F 319 " ideal model delta sigma weight residual 121.54 131.60 -10.06 1.91e+00 2.74e-01 2.78e+01 ... (remaining 61832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.65: 26461 20.65 - 41.29: 1044 41.29 - 61.94: 55 61.94 - 82.58: 16 82.58 - 103.23: 2 Dihedral angle restraints: 27578 sinusoidal: 10985 harmonic: 16593 Sorted by residual: dihedral pdb=" CA ARG N 36 " pdb=" C ARG N 36 " pdb=" N PRO N 37 " pdb=" CA PRO N 37 " ideal model delta harmonic sigma weight residual -180.00 -142.23 -37.77 0 5.00e+00 4.00e-02 5.71e+01 dihedral pdb=" CA HIS N 297 " pdb=" C HIS N 297 " pdb=" N LYS N 298 " pdb=" CA LYS N 298 " ideal model delta harmonic sigma weight residual -180.00 -142.40 -37.60 0 5.00e+00 4.00e-02 5.66e+01 dihedral pdb=" CA VAL N 301 " pdb=" C VAL N 301 " pdb=" N VAL N 302 " pdb=" CA VAL N 302 " ideal model delta harmonic sigma weight residual -180.00 -149.11 -30.89 0 5.00e+00 4.00e-02 3.82e+01 ... (remaining 27575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 6036 0.085 - 0.170: 960 0.170 - 0.256: 73 0.256 - 0.341: 7 0.341 - 0.426: 3 Chirality restraints: 7079 Sorted by residual: chirality pdb=" CB ILE N 544 " pdb=" CA ILE N 544 " pdb=" CG1 ILE N 544 " pdb=" CG2 ILE N 544 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" CB ILE A 226 " pdb=" CA ILE A 226 " pdb=" CG1 ILE A 226 " pdb=" CG2 ILE A 226 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CG LEU N 231 " pdb=" CB LEU N 231 " pdb=" CD1 LEU N 231 " pdb=" CD2 LEU N 231 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 7076 not shown) Planarity restraints: 8046 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 378 " -0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C VAL B 378 " 0.061 2.00e-02 2.50e+03 pdb=" O VAL B 378 " -0.023 2.00e-02 2.50e+03 pdb=" N THR B 379 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 226 " 0.055 5.00e-02 4.00e+02 8.21e-02 1.08e+01 pdb=" N PRO C 227 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO C 227 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 227 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA L 40 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C ALA L 40 " -0.056 2.00e-02 2.50e+03 pdb=" O ALA L 40 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU L 41 " 0.019 2.00e-02 2.50e+03 ... (remaining 8043 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 550 2.66 - 3.22: 39458 3.22 - 3.78: 70199 3.78 - 4.34: 91860 4.34 - 4.90: 154054 Nonbonded interactions: 356121 Sorted by model distance: nonbonded pdb=" O GLU L 36 " pdb=" O LYS L 39 " model vdw 2.095 2.432 nonbonded pdb=" OG1 THR A 235 " pdb="MG MG A 601 " model vdw 2.158 2.170 nonbonded pdb=" O ALA N 538 " pdb=" OG SER N 542 " model vdw 2.193 3.040 nonbonded pdb=" O LEU E 446 " pdb=" OH TYR E 463 " model vdw 2.224 3.040 nonbonded pdb=" OE1 GLU C 38 " pdb=" OH TYR C 52 " model vdw 2.248 3.040 ... (remaining 356116 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 578) selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 5 through 471) selection = (chain 'E' and resid 5 through 471) selection = (chain 'F' and resid 5 through 471) } ncs_group { reference = (chain 'I' and resid 22 through 120) selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 2 through 187) } ncs_group { reference = (chain 'O' and resid 9 through 80) selection = (chain 'P' and resid 9 through 80) selection = (chain 'Q' and resid 9 through 80) selection = (chain 'R' and resid 9 through 80) selection = (chain 'S' and resid 9 through 80) selection = (chain 'T' and resid 9 through 80) selection = (chain 'U' and resid 9 through 80) selection = (chain 'V' and resid 9 through 80) selection = (chain 'W' and resid 9 through 80) selection = chain 'X' selection = (chain 'Y' and resid 9 through 80) selection = (chain 'Z' and resid 9 through 80) } 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: 0.120 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: 0.050 Extract box with map and model: 0.680 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 40.060 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 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 : 0.007 0.115 45669 Z= 0.307 Angle : 1.097 17.551 61839 Z= 0.565 Chirality : 0.061 0.426 7079 Planarity : 0.008 0.082 8046 Dihedral : 10.752 103.230 16985 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.72 % Favored : 93.25 % Rotamer: Outliers : 0.82 % Allowed : 6.33 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.36 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.78 (0.09), residues: 5822 helix: -2.18 (0.07), residues: 3120 sheet: -2.05 (0.20), residues: 574 loop : -2.92 (0.11), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 360 TYR 0.035 0.003 TYR D 411 PHE 0.047 0.003 PHE N 274 TRP 0.037 0.003 TRP A 330 HIS 0.016 0.002 HIS N 561 Details of bonding type rmsd covalent geometry : bond 0.00724 (45668) covalent geometry : angle 1.09686 (61837) SS BOND : bond 0.00694 ( 1) SS BOND : angle 1.00003 ( 2) hydrogen bonds : bond 0.10876 ( 2662) hydrogen bonds : angle 6.18429 ( 8004) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11644 Ramachandran restraints generated. 5822 Oldfield, 0 Emsley, 5822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11644 Ramachandran restraints generated. 5822 Oldfield, 0 Emsley, 5822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1352 residues out of total 4601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 1315 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 TARDY: cannot create tardy model for: "PRO L 146 " (corrupted residue). Skipping it. Corrupt residue: chain: L residue: PRO 146 >>> skipping 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 465 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8664 (mm-40) REVERT: A 469 GLN cc_start: 0.7936 (mt0) cc_final: 0.7596 (pp30) REVERT: A 489 ILE cc_start: 0.9190 (tt) cc_final: 0.8987 (tp) REVERT: B 128 GLU cc_start: 0.8862 (tt0) cc_final: 0.8621 (tt0) REVERT: B 130 ARG cc_start: 0.8677 (pmm-80) cc_final: 0.8040 (ptm-80) REVERT: B 262 MET cc_start: 0.8523 (ptm) cc_final: 0.8253 (ttp) REVERT: B 481 ARG cc_start: 0.8227 (ttt180) cc_final: 0.7735 (ttm110) REVERT: C 43 ASP cc_start: 0.9008 (t0) cc_final: 0.8750 (t0) REVERT: C 152 ASP cc_start: 0.8767 (m-30) cc_final: 0.8480 (t70) REVERT: C 220 MET cc_start: 0.9121 (tpp) cc_final: 0.8740 (tpt) REVERT: C 267 VAL cc_start: 0.9043 (t) cc_final: 0.8810 (m) REVERT: C 442 ASN cc_start: 0.9064 (m-40) cc_final: 0.8833 (m-40) REVERT: C 502 GLU cc_start: 0.8846 (tp30) cc_final: 0.8546 (pt0) REVERT: C 525 GLU cc_start: 0.8566 (tt0) cc_final: 0.8205 (mt-10) REVERT: D 26 ASP cc_start: 0.8926 (m-30) cc_final: 0.8416 (t70) REVERT: D 136 SER cc_start: 0.9183 (t) cc_final: 0.8931 (p) REVERT: D 185 GLU cc_start: 0.8259 (pp20) cc_final: 0.7911 (pm20) REVERT: D 318 ASP cc_start: 0.8112 (t70) cc_final: 0.7883 (t70) REVERT: E 96 ILE cc_start: 0.8756 (mm) cc_final: 0.8296 (pt) REVERT: E 342 GLU cc_start: 0.9365 (tm-30) cc_final: 0.8927 (pm20) REVERT: E 410 ARG cc_start: 0.8517 (mmm160) cc_final: 0.8272 (mtp85) REVERT: E 413 GLN cc_start: 0.8582 (mt0) cc_final: 0.8349 (mp10) REVERT: F 57 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8762 (mp) REVERT: F 77 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8262 (mm-30) REVERT: F 79 VAL cc_start: 0.8950 (m) cc_final: 0.8526 (p) REVERT: F 470 ILE cc_start: 0.6810 (OUTLIER) cc_final: 0.6451 (pp) REVERT: G 9 MET cc_start: 0.8715 (ttp) cc_final: 0.8473 (mmp) REVERT: G 59 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7632 (tp30) REVERT: G 127 SER cc_start: 0.9060 (t) cc_final: 0.8404 (p) REVERT: G 135 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7371 (mm-30) REVERT: G 162 ASN cc_start: 0.8807 (m-40) cc_final: 0.8296 (m110) REVERT: H 8 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7551 (tm-30) REVERT: H 34 GLU cc_start: 0.7938 (tp30) cc_final: 0.7551 (mt-10) REVERT: H 48 ASP cc_start: 0.7240 (t70) cc_final: 0.6490 (t0) REVERT: I 95 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7515 (pt0) REVERT: I 97 LYS cc_start: 0.8259 (mmpt) cc_final: 0.7914 (mmmt) REVERT: I 111 VAL cc_start: 0.6838 (t) cc_final: 0.6441 (p) REVERT: J 5 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8915 (mt-10) REVERT: J 81 GLU cc_start: 0.9084 (tm-30) cc_final: 0.8608 (pp20) REVERT: J 89 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7651 (pm20) REVERT: J 173 ARG cc_start: 0.7485 (mmt90) cc_final: 0.7152 (mtt90) REVERT: K 43 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8178 (tp30) REVERT: K 45 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8308 (tm-30) REVERT: K 46 GLU cc_start: 0.8416 (tm-30) cc_final: 0.7749 (tm-30) REVERT: K 82 GLU cc_start: 0.8598 (tp30) cc_final: 0.8306 (mm-30) REVERT: K 93 GLU cc_start: 0.8691 (tp30) cc_final: 0.8442 (pp20) REVERT: L 8 LEU cc_start: 0.8905 (mt) cc_final: 0.8681 (pp) REVERT: L 35 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8754 (tm-30) REVERT: L 53 TYR cc_start: 0.6716 (t80) cc_final: 0.6255 (t80) REVERT: L 96 GLN cc_start: 0.6919 (mp-120) cc_final: 0.6664 (mp10) REVERT: L 109 LEU cc_start: 0.8563 (tt) cc_final: 0.8163 (pp) REVERT: L 184 GLN cc_start: 0.8718 (pp30) cc_final: 0.8489 (pp30) REVERT: M 59 ARG cc_start: 0.8585 (tmt-80) cc_final: 0.8047 (tmt-80) REVERT: M 111 GLU cc_start: 0.8656 (tp30) cc_final: 0.8359 (tp30) REVERT: M 229 ARG cc_start: 0.8359 (mtt180) cc_final: 0.8025 (mtm180) REVERT: M 285 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7827 (tt) REVERT: M 303 LEU cc_start: 0.7623 (mm) cc_final: 0.7380 (mm) REVERT: N 1 MET cc_start: 0.7661 (ttm) cc_final: 0.7229 (ttm) REVERT: N 22 GLN cc_start: 0.8869 (tp40) cc_final: 0.8498 (tp40) REVERT: N 95 GLN cc_start: 0.9215 (tm130) cc_final: 0.8840 (tp40) REVERT: N 99 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8351 (tm-30) REVERT: N 105 LYS cc_start: 0.8654 (tttt) cc_final: 0.7957 (tptm) REVERT: N 110 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8284 (mt-10) REVERT: N 267 GLU cc_start: 0.8961 (pt0) cc_final: 0.8421 (pp20) REVERT: N 268 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8811 (tp30) REVERT: N 497 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8105 (mt-10) REVERT: N 528 MET cc_start: 0.7599 (tmt) cc_final: 0.7349 (tmm) REVERT: N 547 MET cc_start: 0.8228 (mtm) cc_final: 0.7959 (mtp) REVERT: N 622 ARG cc_start: 0.8863 (ppp-140) cc_final: 0.8496 (ptm160) REVERT: O 61 LEU cc_start: 0.8137 (tm) cc_final: 0.7868 (tm) REVERT: R 52 PHE cc_start: 0.7292 (t80) cc_final: 0.6800 (t80) REVERT: T 52 PHE cc_start: 0.7540 (t80) cc_final: 0.7104 (t80) REVERT: W 61 LEU cc_start: 0.9039 (tm) cc_final: 0.8725 (tp) REVERT: X 25 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7510 (mp) REVERT: Y 14 LEU cc_start: 0.8806 (tp) cc_final: 0.8561 (tp) outliers start: 37 outliers final: 8 residues processed: 1344 average time/residue: 0.3009 time to fit residues: 633.7375 Evaluate side-chains 905 residues out of total 4601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 892 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 470 ILE Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain N residue 379 LEU Chi-restraints excluded: chain N residue 573 ILE Chi-restraints excluded: chain N residue 592 LEU Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 25 LEU Chi-restraints excluded: chain X residue 25 LEU Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 30 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 394 optimal weight: 20.0000 chunk 430 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 265 optimal weight: 5.9990 chunk 523 optimal weight: 10.0000 chunk 497 optimal weight: 10.0000 chunk 414 optimal weight: 6.9990 chunk 310 optimal weight: 20.0000 chunk 488 optimal weight: 20.0000 chunk 366 optimal weight: 8.9990 chunk 223 optimal weight: 2.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN B 316 GLN B 459 GLN C 425 ASN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN E 252 HIS E 363 ASN E 364 ASN E 458 HIS F 166 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 130 HIS L 162 GLN M 52 GLN M 91 ASN N 25 GLN N 250 GLN ** N 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 312 HIS N 386 ASN N 443 HIS ** N 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 557 HIS ** N 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 51 ASN P 77 ASN ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 34 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.147128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.108360 restraints weight = 67761.566| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.26 r_work: 0.3179 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 45669 Z= 0.209 Angle : 0.762 17.282 61839 Z= 0.381 Chirality : 0.047 0.375 7079 Planarity : 0.006 0.069 8046 Dihedral : 6.444 90.397 6464 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.77 % Favored : 94.19 % Rotamer: Outliers : 3.59 % Allowed : 13.21 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.36 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.10), residues: 5822 helix: -0.30 (0.09), residues: 3143 sheet: -1.88 (0.20), residues: 590 loop : -2.45 (0.12), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 76 TYR 0.022 0.002 TYR N 424 PHE 0.025 0.002 PHE N 477 TRP 0.023 0.002 TRP J 100 HIS 0.009 0.001 HIS N 561 Details of bonding type rmsd covalent geometry : bond 0.00490 (45668) covalent geometry : angle 0.76210 (61837) SS BOND : bond 0.00039 ( 1) SS BOND : angle 0.52078 ( 2) hydrogen bonds : bond 0.04903 ( 2662) hydrogen bonds : angle 4.95110 ( 8004) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11644 Ramachandran restraints generated. 5822 Oldfield, 0 Emsley, 5822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11644 Ramachandran restraints generated. 5822 Oldfield, 0 Emsley, 5822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1171 residues out of total 4601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 1008 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO L 146 " (corrupted residue). Skipping it. Corrupt residue: chain: L residue: PRO 146 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 LEU cc_start: 0.9300 (tm) cc_final: 0.8915 (tt) REVERT: A 469 GLN cc_start: 0.7783 (mt0) cc_final: 0.7528 (pp30) REVERT: A 489 ILE cc_start: 0.9191 (tt) cc_final: 0.8914 (tp) REVERT: A 530 ILE cc_start: 0.7874 (tt) cc_final: 0.7670 (tt) REVERT: B 128 GLU cc_start: 0.8904 (tt0) cc_final: 0.8649 (tt0) REVERT: B 130 ARG cc_start: 0.8414 (pmm-80) cc_final: 0.7575 (ptm-80) REVERT: B 481 ARG cc_start: 0.7702 (ttt180) cc_final: 0.7181 (ttm110) REVERT: B 547 ARG cc_start: 0.8153 (mmt-90) cc_final: 0.7663 (mmt180) REVERT: C 96 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7770 (mt-10) REVERT: C 341 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8375 (tt) REVERT: C 393 GLU cc_start: 0.8268 (tt0) cc_final: 0.7991 (tt0) REVERT: C 442 ASN cc_start: 0.9191 (m-40) cc_final: 0.8852 (m-40) REVERT: C 489 ILE cc_start: 0.8875 (mm) cc_final: 0.8661 (mm) REVERT: C 502 GLU cc_start: 0.8554 (tp30) cc_final: 0.8205 (pt0) REVERT: C 525 GLU cc_start: 0.8461 (tt0) cc_final: 0.7843 (mt-10) REVERT: C 547 ARG cc_start: 0.8017 (mmm160) cc_final: 0.7804 (mmm160) REVERT: D 26 ASP cc_start: 0.8592 (m-30) cc_final: 0.8101 (t70) REVERT: D 136 SER cc_start: 0.9341 (t) cc_final: 0.9089 (p) REVERT: D 185 GLU cc_start: 0.7876 (pp20) cc_final: 0.7591 (pm20) REVERT: D 283 TYR cc_start: 0.9227 (m-80) cc_final: 0.8999 (m-80) REVERT: D 318 ASP cc_start: 0.7435 (t70) cc_final: 0.7111 (t70) REVERT: E 96 ILE cc_start: 0.8776 (mm) cc_final: 0.8543 (pt) REVERT: E 269 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8526 (tm-30) REVERT: E 342 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8610 (pm20) REVERT: E 353 ASP cc_start: 0.8869 (p0) cc_final: 0.8629 (p0) REVERT: E 413 GLN cc_start: 0.8383 (mt0) cc_final: 0.8115 (mp10) REVERT: E 445 MET cc_start: 0.8907 (mtp) cc_final: 0.8691 (mtp) REVERT: F 77 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7859 (mm-30) REVERT: F 79 VAL cc_start: 0.9015 (m) cc_final: 0.8258 (p) REVERT: F 420 ARG cc_start: 0.8700 (mtm110) cc_final: 0.8451 (mtm110) REVERT: F 470 ILE cc_start: 0.5974 (OUTLIER) cc_final: 0.5659 (pp) REVERT: G 105 LYS cc_start: 0.5392 (pmtt) cc_final: 0.5054 (pttm) REVERT: G 127 SER cc_start: 0.9053 (t) cc_final: 0.8590 (p) REVERT: G 138 ILE cc_start: 0.8070 (pp) cc_final: 0.7840 (pp) REVERT: G 144 GLU cc_start: 0.8254 (mp0) cc_final: 0.7990 (mp0) REVERT: H 48 ASP cc_start: 0.7139 (t70) cc_final: 0.6374 (t0) REVERT: H 56 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6820 (pm20) REVERT: I 76 ARG cc_start: 0.7811 (ttp80) cc_final: 0.7531 (ttp80) REVERT: I 85 LEU cc_start: 0.8029 (mp) cc_final: 0.7261 (pp) REVERT: I 97 LYS cc_start: 0.8060 (mmpt) cc_final: 0.7758 (mmmt) REVERT: I 117 GLU cc_start: 0.7318 (mm-30) cc_final: 0.7028 (mm-30) REVERT: J 36 GLU cc_start: 0.9003 (mt-10) cc_final: 0.7322 (pt0) REVERT: J 52 GLN cc_start: 0.9007 (tm-30) cc_final: 0.8797 (pp30) REVERT: J 74 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8623 (pp30) REVERT: J 81 GLU cc_start: 0.9088 (tm-30) cc_final: 0.8771 (pp20) REVERT: J 110 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8831 (tm-30) REVERT: K 42 LYS cc_start: 0.8254 (tptp) cc_final: 0.8022 (mttt) REVERT: K 43 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8168 (tp30) REVERT: K 46 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8091 (tm-30) REVERT: K 87 ARG cc_start: 0.7928 (ttp80) cc_final: 0.7580 (ttp80) REVERT: L 35 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8711 (tm-30) REVERT: L 53 TYR cc_start: 0.6783 (t80) cc_final: 0.6171 (t80) REVERT: L 109 LEU cc_start: 0.8130 (tt) cc_final: 0.7813 (pp) REVERT: L 143 GLN cc_start: 0.7423 (tm-30) cc_final: 0.7203 (tm-30) REVERT: L 178 LEU cc_start: 0.8848 (mt) cc_final: 0.8646 (mt) REVERT: L 184 GLN cc_start: 0.8757 (pp30) cc_final: 0.8496 (pp30) REVERT: M 59 ARG cc_start: 0.8515 (tmt-80) cc_final: 0.8024 (tmt-80) REVERT: M 107 ARG cc_start: 0.8545 (mtp85) cc_final: 0.8040 (mtm-85) REVERT: M 138 GLN cc_start: 0.9059 (tm130) cc_final: 0.8676 (tm-30) REVERT: M 205 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.8270 (t80) REVERT: M 279 ASP cc_start: 0.7470 (t0) cc_final: 0.7238 (t0) REVERT: M 303 LEU cc_start: 0.7520 (mm) cc_final: 0.7182 (mm) REVERT: N 99 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8154 (tm-30) REVERT: N 124 ARG cc_start: 0.8918 (tpm170) cc_final: 0.8543 (ttt180) REVERT: N 240 LYS cc_start: 0.8660 (tmtp) cc_final: 0.8448 (tmtt) REVERT: N 267 GLU cc_start: 0.8791 (pt0) cc_final: 0.8242 (pp20) REVERT: N 268 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8557 (tp30) REVERT: N 305 PHE cc_start: 0.8324 (m-10) cc_final: 0.8076 (m-80) REVERT: N 387 GLU cc_start: 0.7870 (tt0) cc_final: 0.7562 (tt0) REVERT: N 497 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7956 (mt-10) REVERT: N 528 MET cc_start: 0.7501 (tmt) cc_final: 0.7224 (tmm) REVERT: N 550 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8573 (mm-30) REVERT: O 51 ASN cc_start: 0.7946 (m110) cc_final: 0.7621 (m-40) REVERT: O 61 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7786 (tm) REVERT: P 25 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7068 (mp) REVERT: T 52 PHE cc_start: 0.7826 (t80) cc_final: 0.7429 (t80) REVERT: V 28 LEU cc_start: 0.8527 (tp) cc_final: 0.8278 (tp) REVERT: V 52 PHE cc_start: 0.6892 (t80) cc_final: 0.6646 (t80) outliers start: 163 outliers final: 83 residues processed: 1098 average time/residue: 0.2823 time to fit residues: 493.3006 Evaluate side-chains 981 residues out of total 4601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 893 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 470 ILE Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain I residue 78 ARG Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain J residue 181 LYS Chi-restraints excluded: chain K residue 36 ARG Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain M residue 63 ARG Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 205 PHE Chi-restraints excluded: chain M residue 253 SER Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 353 VAL Chi-restraints excluded: chain N residue 379 LEU Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain N residue 418 VAL Chi-restraints excluded: chain N residue 422 VAL Chi-restraints excluded: chain N residue 470 PHE Chi-restraints excluded: chain N residue 534 VAL Chi-restraints excluded: chain N residue 537 LEU Chi-restraints excluded: chain N residue 553 THR Chi-restraints excluded: chain N residue 573 ILE Chi-restraints excluded: chain N residue 592 LEU Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 37 ILE Chi-restraints excluded: chain P residue 56 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 70 LEU Chi-restraints excluded: chain T residue 72 ILE Chi-restraints excluded: chain U residue 75 ILE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 30 THR Chi-restraints excluded: chain W residue 51 ASN Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain X residue 72 ILE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain Y residue 19 MET Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 30 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 490 optimal weight: 2.9990 chunk 236 optimal weight: 10.0000 chunk 437 optimal weight: 3.9990 chunk 405 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 515 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 chunk 504 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 572 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 459 GLN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN E 249 HIS E 363 ASN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 GLN ** K 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 GLN M 52 GLN M 65 GLN M 91 ASN N 25 GLN N 386 ASN ** N 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 554 GLN N 557 HIS ** N 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.147059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.108658 restraints weight = 67613.993| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.21 r_work: 0.3184 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 45669 Z= 0.177 Angle : 0.716 13.688 61839 Z= 0.353 Chirality : 0.045 0.326 7079 Planarity : 0.005 0.083 8046 Dihedral : 5.886 87.030 6453 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.69 % Favored : 94.28 % Rotamer: Outliers : 4.39 % Allowed : 15.21 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.36 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.11), residues: 5822 helix: 0.34 (0.09), residues: 3154 sheet: -1.67 (0.21), residues: 575 loop : -2.20 (0.13), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 74 TYR 0.031 0.001 TYR N 424 PHE 0.019 0.001 PHE A 406 TRP 0.017 0.001 TRP L 100 HIS 0.008 0.001 HIS H 84 Details of bonding type rmsd covalent geometry : bond 0.00406 (45668) covalent geometry : angle 0.71595 (61837) SS BOND : bond 0.00068 ( 1) SS BOND : angle 0.44275 ( 2) hydrogen bonds : bond 0.04560 ( 2662) hydrogen bonds : angle 4.74547 ( 8004) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11644 Ramachandran restraints generated. 5822 Oldfield, 0 Emsley, 5822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11644 Ramachandran restraints generated. 5822 Oldfield, 0 Emsley, 5822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1159 residues out of total 4601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 960 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO L 146 " (corrupted residue). Skipping it. Corrupt residue: chain: L residue: PRO 146 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 LEU cc_start: 0.9283 (tm) cc_final: 0.8935 (tt) REVERT: A 469 GLN cc_start: 0.7793 (mt0) cc_final: 0.7484 (pp30) REVERT: A 489 ILE cc_start: 0.9085 (tt) cc_final: 0.8759 (tp) REVERT: B 128 GLU cc_start: 0.8905 (tt0) cc_final: 0.8631 (tt0) REVERT: B 130 ARG cc_start: 0.8337 (pmm-80) cc_final: 0.7481 (ptm-80) REVERT: B 262 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8248 (ttm) REVERT: B 481 ARG cc_start: 0.7582 (ttt180) cc_final: 0.6991 (ttm110) REVERT: B 542 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.6828 (tt) REVERT: C 147 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8796 (pt) REVERT: C 341 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8131 (tt) REVERT: C 393 GLU cc_start: 0.8254 (tt0) cc_final: 0.7962 (tt0) REVERT: C 413 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9254 (tt) REVERT: C 502 GLU cc_start: 0.8605 (tp30) cc_final: 0.8203 (pt0) REVERT: C 525 GLU cc_start: 0.8495 (tt0) cc_final: 0.8036 (mt-10) REVERT: D 26 ASP cc_start: 0.8650 (m-30) cc_final: 0.8060 (t70) REVERT: D 136 SER cc_start: 0.9296 (t) cc_final: 0.9068 (p) REVERT: D 185 GLU cc_start: 0.7791 (pp20) cc_final: 0.7545 (pm20) REVERT: D 283 TYR cc_start: 0.9213 (m-80) cc_final: 0.8973 (m-80) REVERT: D 466 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8182 (ptpp) REVERT: E 96 ILE cc_start: 0.8761 (mm) cc_final: 0.8449 (pt) REVERT: E 269 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8380 (tm-30) REVERT: E 342 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8519 (pm20) REVERT: E 409 ARG cc_start: 0.8325 (ttm110) cc_final: 0.7945 (ttm170) REVERT: E 413 GLN cc_start: 0.8349 (mt0) cc_final: 0.8119 (mp10) REVERT: E 445 MET cc_start: 0.8796 (mtp) cc_final: 0.8584 (mtm) REVERT: F 7 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8189 (mt-10) REVERT: F 77 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7790 (mm-30) REVERT: F 79 VAL cc_start: 0.8980 (m) cc_final: 0.8444 (p) REVERT: G 55 GLN cc_start: 0.8235 (tm130) cc_final: 0.7934 (tp-100) REVERT: G 59 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7221 (tp30) REVERT: G 127 SER cc_start: 0.9127 (t) cc_final: 0.8649 (p) REVERT: G 144 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: G 158 THR cc_start: 0.8744 (m) cc_final: 0.8393 (m) REVERT: H 48 ASP cc_start: 0.7413 (t70) cc_final: 0.6535 (t0) REVERT: I 34 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8894 (mm) REVERT: I 65 LYS cc_start: 0.8458 (pttp) cc_final: 0.8223 (pttp) REVERT: I 97 LYS cc_start: 0.8078 (mmpt) cc_final: 0.7821 (mmmt) REVERT: I 117 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6888 (mm-30) REVERT: J 36 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7944 (mt-10) REVERT: J 49 LEU cc_start: 0.9238 (mt) cc_final: 0.8994 (tt) REVERT: J 81 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8701 (pp20) REVERT: K 42 LYS cc_start: 0.8583 (tptp) cc_final: 0.8336 (tptp) REVERT: K 43 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8303 (tp30) REVERT: K 45 GLU cc_start: 0.8523 (pp20) cc_final: 0.8204 (pp20) REVERT: K 73 TYR cc_start: 0.7610 (m-80) cc_final: 0.7170 (m-10) REVERT: K 87 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7621 (ttp80) REVERT: L 35 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8689 (tm-30) REVERT: L 109 LEU cc_start: 0.7998 (tt) cc_final: 0.7633 (pp) REVERT: L 130 HIS cc_start: 0.8467 (m170) cc_final: 0.8167 (m-70) REVERT: L 143 GLN cc_start: 0.7497 (tm-30) cc_final: 0.7229 (tm-30) REVERT: M 52 GLN cc_start: 0.8359 (tm130) cc_final: 0.7926 (mm110) REVERT: M 59 ARG cc_start: 0.8459 (tmt-80) cc_final: 0.8044 (tmt-80) REVERT: M 138 GLN cc_start: 0.8925 (tm130) cc_final: 0.8529 (tm-30) REVERT: M 205 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.8311 (t80) REVERT: M 262 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7091 (tm-30) REVERT: M 279 ASP cc_start: 0.7269 (t0) cc_final: 0.7061 (t0) REVERT: M 303 LEU cc_start: 0.7451 (mm) cc_final: 0.7144 (mm) REVERT: N 19 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7293 (tm-30) REVERT: N 21 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8499 (tt) REVERT: N 57 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8294 (mt-10) REVERT: N 99 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8109 (tm-30) REVERT: N 110 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8220 (mt-10) REVERT: N 124 ARG cc_start: 0.8934 (tpm170) cc_final: 0.8513 (ttt180) REVERT: N 267 GLU cc_start: 0.8848 (pt0) cc_final: 0.8239 (pp20) REVERT: N 278 LEU cc_start: 0.7908 (pt) cc_final: 0.7495 (pp) REVERT: N 387 GLU cc_start: 0.7910 (tt0) cc_final: 0.7621 (tt0) REVERT: N 423 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8438 (tt) REVERT: N 505 LEU cc_start: 0.9212 (tp) cc_final: 0.8927 (tt) REVERT: N 528 MET cc_start: 0.7465 (tmt) cc_final: 0.7170 (tmm) REVERT: N 550 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8486 (mm-30) REVERT: O 51 ASN cc_start: 0.7929 (m110) cc_final: 0.7598 (m-40) REVERT: O 61 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7791 (tm) REVERT: P 14 LEU cc_start: 0.8147 (tp) cc_final: 0.7926 (tp) REVERT: P 25 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7017 (mp) REVERT: R 52 PHE cc_start: 0.7570 (t80) cc_final: 0.7356 (t80) REVERT: T 52 PHE cc_start: 0.7806 (t80) cc_final: 0.7355 (t80) REVERT: T 67 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8141 (tp) REVERT: V 28 LEU cc_start: 0.8452 (tp) cc_final: 0.8166 (tp) REVERT: V 52 PHE cc_start: 0.6790 (t80) cc_final: 0.6569 (t80) REVERT: Y 79 ARG cc_start: 0.7674 (tpp80) cc_final: 0.7090 (tpp80) REVERT: Y 80 LEU cc_start: 0.6440 (OUTLIER) cc_final: 0.6022 (tt) outliers start: 199 outliers final: 107 residues processed: 1076 average time/residue: 0.2787 time to fit residues: 478.6632 Evaluate side-chains 1004 residues out of total 4601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 882 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 466 LYS Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 78 ARG Chi-restraints excluded: chain I residue 116 LYS Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain M residue 63 ARG Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 175 ASP Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 203 THR Chi-restraints excluded: chain M residue 205 PHE Chi-restraints excluded: chain M residue 253 SER Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 379 LEU Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain N residue 417 THR Chi-restraints excluded: chain N residue 418 VAL Chi-restraints excluded: chain N residue 422 VAL Chi-restraints excluded: chain N residue 423 ILE Chi-restraints excluded: chain N residue 470 PHE Chi-restraints excluded: chain N residue 519 LEU Chi-restraints excluded: chain N residue 534 VAL Chi-restraints excluded: chain N residue 537 LEU Chi-restraints excluded: chain N residue 553 THR Chi-restraints excluded: chain N residue 573 ILE Chi-restraints excluded: chain N residue 592 LEU Chi-restraints excluded: chain N residue 608 ILE Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 52 PHE Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 56 LEU Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 67 ILE Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 70 LEU Chi-restraints excluded: chain T residue 72 ILE Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain V residue 72 ILE Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 30 THR Chi-restraints excluded: chain W residue 51 ASN Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain Y residue 19 MET Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Y residue 80 LEU Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain Z residue 67 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 153 optimal weight: 3.9990 chunk 47 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 547 optimal weight: 9.9990 chunk 329 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 406 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 504 optimal weight: 10.0000 chunk 193 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 GLN A 397 GLN B 459 GLN C 316 GLN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 HIS ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN ** J 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 GLN N 25 GLN N 386 ASN N 452 HIS N 554 GLN ** N 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.145133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.105752 restraints weight = 68429.234| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.27 r_work: 0.3143 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 45669 Z= 0.221 Angle : 0.735 12.529 61839 Z= 0.363 Chirality : 0.047 0.309 7079 Planarity : 0.005 0.129 8046 Dihedral : 5.702 85.216 6449 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.27 % Favored : 93.70 % Rotamer: Outliers : 5.03 % Allowed : 16.34 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.36 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.11), residues: 5822 helix: 0.56 (0.09), residues: 3158 sheet: -1.60 (0.21), residues: 567 loop : -2.04 (0.13), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 88 TYR 0.042 0.002 TYR N 424 PHE 0.022 0.002 PHE A 406 TRP 0.030 0.002 TRP F 471 HIS 0.007 0.001 HIS H 84 Details of bonding type rmsd covalent geometry : bond 0.00525 (45668) covalent geometry : angle 0.73533 (61837) SS BOND : bond 0.00030 ( 1) SS BOND : angle 0.47921 ( 2) hydrogen bonds : bond 0.04617 ( 2662) hydrogen bonds : angle 4.70507 ( 8004) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11644 Ramachandran restraints generated. 5822 Oldfield, 0 Emsley, 5822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11644 Ramachandran restraints generated. 5822 Oldfield, 0 Emsley, 5822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1141 residues out of total 4601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 228 poor density : 913 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO L 146 " (corrupted residue). Skipping it. Corrupt residue: chain: L residue: PRO 146 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9028 (tt) REVERT: A 412 SER cc_start: 0.9075 (m) cc_final: 0.8835 (t) REVERT: A 469 GLN cc_start: 0.7953 (mt0) cc_final: 0.7649 (pp30) REVERT: A 489 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8863 (tt) REVERT: A 520 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8687 (mm) REVERT: A 571 GLN cc_start: 0.7365 (mt0) cc_final: 0.7163 (mt0) REVERT: B 128 GLU cc_start: 0.8802 (tt0) cc_final: 0.8500 (tt0) REVERT: B 130 ARG cc_start: 0.8365 (pmm-80) cc_final: 0.7633 (ptm-80) REVERT: B 481 ARG cc_start: 0.7718 (ttt180) cc_final: 0.7202 (ttm110) REVERT: B 542 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.6821 (tt) REVERT: C 147 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8876 (pt) REVERT: C 393 GLU cc_start: 0.8237 (tt0) cc_final: 0.7938 (tt0) REVERT: C 450 LEU cc_start: 0.9271 (tp) cc_final: 0.9060 (tp) REVERT: C 502 GLU cc_start: 0.8579 (tp30) cc_final: 0.8229 (pt0) REVERT: C 525 GLU cc_start: 0.8492 (tt0) cc_final: 0.8044 (mt-10) REVERT: D 136 SER cc_start: 0.9359 (t) cc_final: 0.9102 (p) REVERT: D 185 GLU cc_start: 0.7858 (pp20) cc_final: 0.7547 (pm20) REVERT: D 283 TYR cc_start: 0.9253 (m-80) cc_final: 0.9013 (m-80) REVERT: D 466 LYS cc_start: 0.8509 (mtmt) cc_final: 0.8148 (ptpp) REVERT: E 96 ILE cc_start: 0.8830 (mm) cc_final: 0.8588 (pt) REVERT: E 342 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8523 (pm20) REVERT: E 409 ARG cc_start: 0.8355 (ttm110) cc_final: 0.7915 (ttm170) REVERT: E 413 GLN cc_start: 0.8400 (mt0) cc_final: 0.8144 (mp10) REVERT: F 77 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7919 (mm-30) REVERT: F 79 VAL cc_start: 0.9107 (m) cc_final: 0.8593 (p) REVERT: G 59 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7257 (tp30) REVERT: G 127 SER cc_start: 0.9166 (t) cc_final: 0.8665 (p) REVERT: G 144 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7883 (tt0) REVERT: H 48 ASP cc_start: 0.7394 (t70) cc_final: 0.6479 (t0) REVERT: I 65 LYS cc_start: 0.8473 (pttp) cc_final: 0.8257 (pttp) REVERT: I 73 TYR cc_start: 0.8653 (t80) cc_final: 0.7613 (t80) REVERT: I 74 ARG cc_start: 0.8458 (mmp80) cc_final: 0.8196 (mmp80) REVERT: I 85 LEU cc_start: 0.7799 (mt) cc_final: 0.7390 (pp) REVERT: I 97 LYS cc_start: 0.8141 (mmpt) cc_final: 0.7826 (mmmt) REVERT: I 117 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7006 (mm-30) REVERT: J 49 LEU cc_start: 0.9352 (mt) cc_final: 0.8819 (tt) REVERT: J 52 GLN cc_start: 0.9555 (pp30) cc_final: 0.9104 (pp30) REVERT: J 81 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8621 (pp20) REVERT: J 110 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8783 (tm-30) REVERT: K 42 LYS cc_start: 0.8544 (tptp) cc_final: 0.8281 (tptp) REVERT: K 43 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8384 (tp30) REVERT: K 82 GLU cc_start: 0.8205 (tp30) cc_final: 0.7838 (mm-30) REVERT: K 87 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7678 (ttp80) REVERT: L 35 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8716 (tm-30) REVERT: L 109 LEU cc_start: 0.7979 (tt) cc_final: 0.7541 (pp) REVERT: L 130 HIS cc_start: 0.8353 (m170) cc_final: 0.8075 (m-70) REVERT: L 143 GLN cc_start: 0.7421 (tm-30) cc_final: 0.6679 (tm-30) REVERT: M 52 GLN cc_start: 0.8289 (tm130) cc_final: 0.7868 (mm110) REVERT: M 59 ARG cc_start: 0.8516 (tmt-80) cc_final: 0.8092 (tmt-80) REVERT: M 114 LEU cc_start: 0.8773 (mt) cc_final: 0.8457 (mt) REVERT: M 138 GLN cc_start: 0.8982 (tm130) cc_final: 0.8577 (tm-30) REVERT: M 229 ARG cc_start: 0.8107 (mtt180) cc_final: 0.7896 (mtm180) REVERT: M 262 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7216 (tm-30) REVERT: M 279 ASP cc_start: 0.7307 (t0) cc_final: 0.7084 (t0) REVERT: M 303 LEU cc_start: 0.7574 (mm) cc_final: 0.7229 (mm) REVERT: M 308 TYR cc_start: 0.8499 (t80) cc_final: 0.8294 (t80) REVERT: N 19 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7326 (tm-30) REVERT: N 21 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8533 (tt) REVERT: N 57 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8231 (mt-10) REVERT: N 99 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8117 (tm-30) REVERT: N 110 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8214 (mt-10) REVERT: N 124 ARG cc_start: 0.8938 (tpm170) cc_final: 0.8509 (ttt180) REVERT: N 267 GLU cc_start: 0.8842 (pt0) cc_final: 0.8301 (pp20) REVERT: N 268 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8418 (tp30) REVERT: N 278 LEU cc_start: 0.7821 (pt) cc_final: 0.7532 (pp) REVERT: N 387 GLU cc_start: 0.7882 (tt0) cc_final: 0.7649 (tt0) REVERT: N 505 LEU cc_start: 0.9248 (tp) cc_final: 0.8964 (tt) REVERT: N 528 MET cc_start: 0.7550 (tmt) cc_final: 0.7238 (tmm) REVERT: N 541 MET cc_start: 0.7925 (ttm) cc_final: 0.7060 (ttm) REVERT: N 550 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8367 (mm-30) REVERT: O 51 ASN cc_start: 0.7974 (m110) cc_final: 0.7668 (m-40) REVERT: O 61 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7967 (tm) REVERT: P 14 LEU cc_start: 0.8325 (tp) cc_final: 0.8106 (tp) REVERT: P 25 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7261 (mp) REVERT: T 52 PHE cc_start: 0.7899 (t80) cc_final: 0.7431 (t80) REVERT: T 67 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8159 (tp) REVERT: U 14 LEU cc_start: 0.8443 (tp) cc_final: 0.8130 (tp) REVERT: V 28 LEU cc_start: 0.8531 (tp) cc_final: 0.8250 (tp) REVERT: V 52 PHE cc_start: 0.6914 (t80) cc_final: 0.6657 (t80) REVERT: X 21 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7908 (tt) REVERT: Y 80 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.6079 (tt) outliers start: 228 outliers final: 145 residues processed: 1054 average time/residue: 0.2747 time to fit residues: 466.8348 Evaluate side-chains 1048 residues out of total 4601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 891 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 78 ARG Chi-restraints excluded: chain I residue 116 LYS Chi-restraints excluded: chain J residue 181 LYS Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 63 ARG Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 175 ASP Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 203 THR Chi-restraints excluded: chain M residue 253 SER Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain N residue 418 VAL Chi-restraints excluded: chain N residue 422 VAL Chi-restraints excluded: chain N residue 431 PHE Chi-restraints excluded: chain N residue 466 LEU Chi-restraints excluded: chain N residue 470 PHE Chi-restraints excluded: chain N residue 519 LEU Chi-restraints excluded: chain N residue 534 VAL Chi-restraints excluded: chain N residue 537 LEU Chi-restraints excluded: chain N residue 553 THR Chi-restraints excluded: chain N residue 573 ILE Chi-restraints excluded: chain N residue 592 LEU Chi-restraints excluded: chain N residue 608 ILE Chi-restraints excluded: chain N residue 609 LEU Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 52 PHE Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 56 LEU Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain S residue 17 VAL Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 67 ILE Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 70 LEU Chi-restraints excluded: chain T residue 72 ILE Chi-restraints excluded: chain V residue 58 PHE Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain V residue 72 ILE Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 30 THR Chi-restraints excluded: chain W residue 51 ASN Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain X residue 19 MET Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain Y residue 19 MET Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Y residue 80 LEU Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain Z residue 67 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 281 optimal weight: 4.9990 chunk 252 optimal weight: 5.9990 chunk 285 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 414 optimal weight: 20.0000 chunk 187 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 301 optimal weight: 10.0000 chunk 366 optimal weight: 30.0000 chunk 175 optimal weight: 10.0000 chunk 506 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 GLN A 397 GLN B 459 GLN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 GLN M 91 ASN M 97 GLN M 126 GLN N 25 GLN ** N 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 386 ASN N 554 GLN ** N 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.146226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.106950 restraints weight = 68052.889| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.26 r_work: 0.3167 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 45669 Z= 0.181 Angle : 0.711 14.538 61839 Z= 0.348 Chirality : 0.045 0.242 7079 Planarity : 0.005 0.094 8046 Dihedral : 5.523 82.157 6447 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.79 % Favored : 94.18 % Rotamer: Outliers : 5.42 % Allowed : 16.78 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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 are not related in a simple way. whole: -0.65 (0.11), residues: 5822 helix: 0.77 (0.09), residues: 3145 sheet: -1.53 (0.21), residues: 557 loop : -1.94 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 420 TYR 0.029 0.001 TYR N 424 PHE 0.020 0.001 PHE A 406 TRP 0.016 0.001 TRP L 100 HIS 0.007 0.001 HIS H 84 Details of bonding type rmsd covalent geometry : bond 0.00423 (45668) covalent geometry : angle 0.71061 (61837) SS BOND : bond 0.00051 ( 1) SS BOND : angle 0.37597 ( 2) hydrogen bonds : bond 0.04418 ( 2662) hydrogen bonds : angle 4.62350 ( 8004) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11644 Ramachandran restraints generated. 5822 Oldfield, 0 Emsley, 5822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11644 Ramachandran restraints generated. 5822 Oldfield, 0 Emsley, 5822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1185 residues out of total 4601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 246 poor density : 939 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO L 146 " (corrupted residue). Skipping it. Corrupt residue: chain: L residue: PRO 146 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.9048 (t0) cc_final: 0.8827 (t0) REVERT: A 400 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8988 (tt) REVERT: A 412 SER cc_start: 0.9055 (m) cc_final: 0.8816 (t) REVERT: A 469 GLN cc_start: 0.7996 (mt0) cc_final: 0.7671 (pp30) REVERT: A 489 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8892 (tt) REVERT: A 520 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8658 (mm) REVERT: A 571 GLN cc_start: 0.7412 (mt0) cc_final: 0.7183 (mt0) REVERT: B 128 GLU cc_start: 0.8757 (tt0) cc_final: 0.8468 (tt0) REVERT: B 130 ARG cc_start: 0.8401 (pmm-80) cc_final: 0.7673 (ptm-80) REVERT: B 166 TYR cc_start: 0.8346 (m-10) cc_final: 0.7973 (m-10) REVERT: B 287 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8594 (tt) REVERT: B 481 ARG cc_start: 0.7696 (ttt180) cc_final: 0.7176 (ttm110) REVERT: B 542 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.6740 (tt) REVERT: C 147 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8861 (pt) REVERT: C 156 ARG cc_start: 0.8465 (mtp-110) cc_final: 0.8108 (mtp-110) REVERT: C 341 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8249 (tt) REVERT: C 393 GLU cc_start: 0.8267 (tt0) cc_final: 0.7920 (tt0) REVERT: C 441 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8263 (mp0) REVERT: C 450 LEU cc_start: 0.9219 (tp) cc_final: 0.8988 (tp) REVERT: C 502 GLU cc_start: 0.8579 (tp30) cc_final: 0.8235 (pt0) REVERT: C 525 GLU cc_start: 0.8483 (tt0) cc_final: 0.8000 (mt-10) REVERT: D 26 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.7783 (t70) REVERT: D 136 SER cc_start: 0.9335 (t) cc_final: 0.9093 (p) REVERT: D 185 GLU cc_start: 0.7840 (pp20) cc_final: 0.7512 (pm20) REVERT: D 283 TYR cc_start: 0.9247 (m-80) cc_final: 0.9023 (m-80) REVERT: D 353 ASP cc_start: 0.8316 (t70) cc_final: 0.8090 (t0) REVERT: D 466 LYS cc_start: 0.8476 (mtmt) cc_final: 0.8126 (ptpp) REVERT: E 96 ILE cc_start: 0.8815 (mm) cc_final: 0.8594 (pt) REVERT: E 269 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8423 (tm-30) REVERT: E 342 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8531 (pm20) REVERT: E 409 ARG cc_start: 0.8362 (ttm110) cc_final: 0.7941 (mtm-85) REVERT: E 413 GLN cc_start: 0.8401 (mt0) cc_final: 0.8158 (mp10) REVERT: F 57 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.9023 (mp) REVERT: F 77 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7953 (mm-30) REVERT: F 79 VAL cc_start: 0.9078 (m) cc_final: 0.8548 (p) REVERT: F 361 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8811 (pp) REVERT: F 429 ASN cc_start: 0.8620 (t0) cc_final: 0.8417 (t0) REVERT: G 55 GLN cc_start: 0.8397 (tm-30) cc_final: 0.7969 (tp-100) REVERT: G 59 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7156 (tp30) REVERT: G 127 SER cc_start: 0.9199 (t) cc_final: 0.8202 (p) REVERT: G 144 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7946 (tt0) REVERT: G 200 LYS cc_start: 0.7612 (mttm) cc_final: 0.7401 (mttm) REVERT: H 48 ASP cc_start: 0.7372 (t70) cc_final: 0.6490 (t0) REVERT: I 31 LYS cc_start: 0.8741 (ptpp) cc_final: 0.8527 (ptpp) REVERT: I 65 LYS cc_start: 0.8451 (pttp) cc_final: 0.8245 (pttp) REVERT: I 85 LEU cc_start: 0.7848 (mt) cc_final: 0.7496 (pp) REVERT: I 97 LYS cc_start: 0.8178 (mmpt) cc_final: 0.7883 (mmmt) REVERT: I 117 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7007 (mm-30) REVERT: J 49 LEU cc_start: 0.9322 (mt) cc_final: 0.9034 (tt) REVERT: J 59 ARG cc_start: 0.9017 (ttp80) cc_final: 0.8730 (ttp80) REVERT: J 81 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8748 (pp20) REVERT: J 89 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7255 (pm20) REVERT: J 110 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8761 (tm-30) REVERT: K 43 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8295 (tp30) REVERT: K 82 GLU cc_start: 0.8174 (tp30) cc_final: 0.7827 (mm-30) REVERT: K 87 ARG cc_start: 0.7994 (ttp80) cc_final: 0.7661 (ttp80) REVERT: L 31 LYS cc_start: 0.9267 (ptpp) cc_final: 0.8930 (ptpp) REVERT: L 35 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8731 (tm-30) REVERT: L 109 LEU cc_start: 0.7945 (tt) cc_final: 0.7500 (pp) REVERT: L 143 GLN cc_start: 0.7421 (tm-30) cc_final: 0.6664 (tm-30) REVERT: M 52 GLN cc_start: 0.8350 (tm130) cc_final: 0.7979 (mm110) REVERT: M 59 ARG cc_start: 0.8409 (tmt-80) cc_final: 0.7997 (tmt-80) REVERT: M 114 LEU cc_start: 0.8712 (mt) cc_final: 0.8422 (mt) REVERT: M 138 GLN cc_start: 0.8928 (tm130) cc_final: 0.8521 (tm-30) REVERT: M 229 ARG cc_start: 0.8059 (mtt180) cc_final: 0.7413 (mtm180) REVERT: M 262 GLU cc_start: 0.7425 (tm-30) cc_final: 0.7083 (tm-30) REVERT: M 279 ASP cc_start: 0.7307 (t0) cc_final: 0.7097 (t0) REVERT: M 303 LEU cc_start: 0.7555 (mm) cc_final: 0.7256 (mm) REVERT: N 21 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8573 (tt) REVERT: N 57 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8210 (mt-10) REVERT: N 99 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8168 (tm-30) REVERT: N 110 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8193 (mt-10) REVERT: N 267 GLU cc_start: 0.8830 (pt0) cc_final: 0.8298 (pp20) REVERT: N 268 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8383 (tp30) REVERT: N 278 LEU cc_start: 0.7739 (pt) cc_final: 0.7440 (pp) REVERT: N 387 GLU cc_start: 0.7896 (tt0) cc_final: 0.7654 (tt0) REVERT: N 505 LEU cc_start: 0.9259 (tp) cc_final: 0.8977 (tt) REVERT: N 528 MET cc_start: 0.7437 (tmt) cc_final: 0.7100 (tmm) REVERT: N 559 LEU cc_start: 0.9113 (tt) cc_final: 0.8882 (mp) REVERT: O 51 ASN cc_start: 0.7935 (m110) cc_final: 0.7622 (m-40) REVERT: O 61 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7983 (tm) REVERT: P 14 LEU cc_start: 0.8305 (tp) cc_final: 0.8060 (tp) REVERT: P 25 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7204 (mp) REVERT: R 52 PHE cc_start: 0.7527 (t80) cc_final: 0.7134 (t80) REVERT: T 52 PHE cc_start: 0.7886 (t80) cc_final: 0.7417 (t80) REVERT: T 67 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8129 (tp) REVERT: U 14 LEU cc_start: 0.8394 (tp) cc_final: 0.8102 (tp) REVERT: V 28 LEU cc_start: 0.8523 (tp) cc_final: 0.8239 (tp) REVERT: V 52 PHE cc_start: 0.6882 (t80) cc_final: 0.6555 (t80) REVERT: X 21 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7907 (tt) REVERT: Y 80 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6381 (tt) outliers start: 246 outliers final: 161 residues processed: 1088 average time/residue: 0.2710 time to fit residues: 476.0873 Evaluate side-chains 1069 residues out of total 4601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 889 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 116 LYS Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 63 ARG Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 175 ASP Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 203 THR Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 253 SER Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 263 LEU Chi-restraints excluded: chain N residue 407 VAL Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain N residue 418 VAL Chi-restraints excluded: chain N residue 422 VAL Chi-restraints excluded: chain N residue 431 PHE Chi-restraints excluded: chain N residue 466 LEU Chi-restraints excluded: chain N residue 470 PHE Chi-restraints excluded: chain N residue 519 LEU Chi-restraints excluded: chain N residue 529 TYR Chi-restraints excluded: chain N residue 534 VAL Chi-restraints excluded: chain N residue 537 LEU Chi-restraints excluded: chain N residue 547 MET Chi-restraints excluded: chain N residue 553 THR Chi-restraints excluded: chain N residue 573 ILE Chi-restraints excluded: chain N residue 592 LEU Chi-restraints excluded: chain N residue 609 LEU Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 52 PHE Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 56 LEU Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 67 ILE Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 70 LEU Chi-restraints excluded: chain T residue 72 ILE Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 70 LEU Chi-restraints excluded: chain V residue 58 PHE Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain V residue 72 ILE Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 51 ASN Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain X residue 19 MET Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain Y residue 19 MET Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Y residue 80 LEU Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain Z residue 67 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 6 optimal weight: 5.9990 chunk 376 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 282 optimal weight: 4.9990 chunk 408 optimal weight: 40.0000 chunk 536 optimal weight: 6.9990 chunk 571 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 195 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 353 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 GLN G 162 ASN ** K 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 91 ASN M 126 GLN N 25 GLN ** N 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 51 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 = 0.3800 r_free = 0.3800 target = 0.145210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.105898 restraints weight = 68502.122| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.27 r_work: 0.3140 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 45669 Z= 0.210 Angle : 0.731 15.326 61839 Z= 0.359 Chirality : 0.046 0.204 7079 Planarity : 0.005 0.089 8046 Dihedral : 5.497 81.514 6447 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.20 % Favored : 93.77 % Rotamer: Outliers : 5.34 % Allowed : 17.95 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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 are not related in a simple way. whole: -0.60 (0.11), residues: 5822 helix: 0.80 (0.09), residues: 3158 sheet: -1.47 (0.21), residues: 563 loop : -1.92 (0.13), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 50 TYR 0.043 0.002 TYR N 424 PHE 0.023 0.001 PHE A 406 TRP 0.017 0.001 TRP L 100 HIS 0.008 0.001 HIS H 84 Details of bonding type rmsd covalent geometry : bond 0.00499 (45668) covalent geometry : angle 0.73060 (61837) SS BOND : bond 0.00034 ( 1) SS BOND : angle 0.40290 ( 2) hydrogen bonds : bond 0.04499 ( 2662) hydrogen bonds : angle 4.63689 ( 8004) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11644 Ramachandran restraints generated. 5822 Oldfield, 0 Emsley, 5822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11644 Ramachandran restraints generated. 5822 Oldfield, 0 Emsley, 5822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1164 residues out of total 4601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 922 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO L 146 " (corrupted residue). Skipping it. Corrupt residue: chain: L residue: PRO 146 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.9077 (t0) cc_final: 0.8820 (t0) REVERT: A 400 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9029 (tt) REVERT: A 412 SER cc_start: 0.9069 (m) cc_final: 0.8833 (t) REVERT: A 469 GLN cc_start: 0.8124 (mt0) cc_final: 0.7705 (pp30) REVERT: A 489 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8820 (tt) REVERT: A 520 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8701 (mm) REVERT: A 571 GLN cc_start: 0.7486 (mt0) cc_final: 0.7251 (mt0) REVERT: B 128 GLU cc_start: 0.8735 (tt0) cc_final: 0.8429 (tt0) REVERT: B 130 ARG cc_start: 0.8332 (pmm-80) cc_final: 0.7566 (ptm-80) REVERT: B 287 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8748 (tt) REVERT: B 481 ARG cc_start: 0.7723 (ttt180) cc_final: 0.7199 (ttm110) REVERT: B 542 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.6731 (tt) REVERT: C 147 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8893 (pt) REVERT: C 341 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8228 (tt) REVERT: C 393 GLU cc_start: 0.8294 (tt0) cc_final: 0.7957 (tt0) REVERT: C 450 LEU cc_start: 0.9240 (tp) cc_final: 0.8997 (tp) REVERT: C 502 GLU cc_start: 0.8592 (tp30) cc_final: 0.8279 (pt0) REVERT: C 525 GLU cc_start: 0.8492 (tt0) cc_final: 0.8012 (mt-10) REVERT: D 136 SER cc_start: 0.9358 (t) cc_final: 0.9101 (p) REVERT: D 185 GLU cc_start: 0.7826 (pp20) cc_final: 0.7489 (pm20) REVERT: D 283 TYR cc_start: 0.9259 (m-80) cc_final: 0.9025 (m-80) REVERT: D 353 ASP cc_start: 0.8326 (t70) cc_final: 0.8083 (t0) REVERT: D 466 LYS cc_start: 0.8443 (mtmt) cc_final: 0.8101 (ptpp) REVERT: E 96 ILE cc_start: 0.8805 (mm) cc_final: 0.8591 (pt) REVERT: E 269 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8345 (tm-30) REVERT: E 342 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8526 (pm20) REVERT: E 409 ARG cc_start: 0.8369 (ttm110) cc_final: 0.7877 (mtm-85) REVERT: E 413 GLN cc_start: 0.8410 (mt0) cc_final: 0.8167 (mp10) REVERT: F 7 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8091 (mp0) REVERT: F 57 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.9028 (mp) REVERT: F 77 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7950 (mm-30) REVERT: F 79 VAL cc_start: 0.9080 (m) cc_final: 0.8541 (p) REVERT: F 361 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8936 (pp) REVERT: G 59 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7187 (tp30) REVERT: G 128 ARG cc_start: 0.7880 (mmp80) cc_final: 0.7473 (mmp80) REVERT: G 144 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7936 (tt0) REVERT: H 48 ASP cc_start: 0.7385 (t70) cc_final: 0.6467 (t0) REVERT: I 31 LYS cc_start: 0.8781 (ptpp) cc_final: 0.8513 (ptpp) REVERT: I 36 ARG cc_start: 0.7611 (ttp80) cc_final: 0.7339 (ttp80) REVERT: I 73 TYR cc_start: 0.8470 (t80) cc_final: 0.8053 (t80) REVERT: I 74 ARG cc_start: 0.8274 (mmp80) cc_final: 0.7974 (mmp80) REVERT: I 78 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8274 (ppp-140) REVERT: I 85 LEU cc_start: 0.7828 (mt) cc_final: 0.7499 (pp) REVERT: I 97 LYS cc_start: 0.8208 (mmpt) cc_final: 0.7897 (mmmt) REVERT: J 36 GLU cc_start: 0.8599 (pp20) cc_final: 0.7966 (pp20) REVERT: J 52 GLN cc_start: 0.9455 (pp30) cc_final: 0.8861 (pp30) REVERT: J 59 ARG cc_start: 0.9016 (ttp80) cc_final: 0.8760 (ttp80) REVERT: J 88 ARG cc_start: 0.9017 (mtm-85) cc_final: 0.8459 (mtm-85) REVERT: J 110 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8858 (tm-30) REVERT: J 175 TRP cc_start: 0.6709 (t-100) cc_final: 0.5797 (t-100) REVERT: K 43 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8217 (tp30) REVERT: K 82 GLU cc_start: 0.8196 (tp30) cc_final: 0.7874 (mm-30) REVERT: K 87 ARG cc_start: 0.7998 (ttp80) cc_final: 0.7689 (ttp80) REVERT: K 115 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8203 (mm) REVERT: K 116 LYS cc_start: 0.8620 (ptpp) cc_final: 0.8402 (ptpp) REVERT: L 31 LYS cc_start: 0.9321 (ptpp) cc_final: 0.8983 (ptpp) REVERT: L 35 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8666 (tm-30) REVERT: L 109 LEU cc_start: 0.7956 (tt) cc_final: 0.7437 (pp) REVERT: L 143 GLN cc_start: 0.7432 (tm-30) cc_final: 0.6682 (tm-30) REVERT: M 31 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7063 (mp) REVERT: M 52 GLN cc_start: 0.8375 (tm130) cc_final: 0.8013 (mm110) REVERT: M 59 ARG cc_start: 0.8414 (tmt-80) cc_final: 0.8002 (tmt-80) REVERT: M 114 LEU cc_start: 0.8667 (mt) cc_final: 0.8378 (mt) REVERT: M 138 GLN cc_start: 0.8937 (tm130) cc_final: 0.8519 (tm-30) REVERT: M 262 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7109 (tm-30) REVERT: M 303 LEU cc_start: 0.7564 (mm) cc_final: 0.7234 (mm) REVERT: N 19 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7537 (tm-30) REVERT: N 21 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8597 (tt) REVERT: N 57 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8182 (mt-10) REVERT: N 99 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8162 (tm-30) REVERT: N 267 GLU cc_start: 0.8806 (pt0) cc_final: 0.7900 (pp20) REVERT: N 268 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8335 (tp30) REVERT: N 278 LEU cc_start: 0.7760 (pt) cc_final: 0.7546 (pp) REVERT: N 459 THR cc_start: 0.8597 (m) cc_final: 0.8382 (t) REVERT: N 505 LEU cc_start: 0.9238 (tp) cc_final: 0.8927 (tt) REVERT: N 528 MET cc_start: 0.7427 (tmt) cc_final: 0.7062 (tmm) REVERT: N 559 LEU cc_start: 0.9153 (tt) cc_final: 0.8895 (mp) REVERT: O 51 ASN cc_start: 0.7944 (m110) cc_final: 0.7631 (m-40) REVERT: O 61 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8077 (tm) REVERT: P 25 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7029 (mp) REVERT: R 10 LEU cc_start: 0.8094 (tp) cc_final: 0.7868 (tp) REVERT: R 52 PHE cc_start: 0.7582 (t80) cc_final: 0.7375 (t80) REVERT: T 52 PHE cc_start: 0.7904 (t80) cc_final: 0.7416 (t80) REVERT: T 67 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8137 (tp) REVERT: U 14 LEU cc_start: 0.8412 (tp) cc_final: 0.8116 (tp) REVERT: V 28 LEU cc_start: 0.8514 (tp) cc_final: 0.8225 (tp) REVERT: V 52 PHE cc_start: 0.6944 (t80) cc_final: 0.6622 (t80) REVERT: Y 79 ARG cc_start: 0.7803 (tpp80) cc_final: 0.6818 (tpp80) REVERT: Y 80 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6554 (tt) outliers start: 242 outliers final: 177 residues processed: 1071 average time/residue: 0.2766 time to fit residues: 479.9943 Evaluate side-chains 1079 residues out of total 4601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 884 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 78 ARG Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 97 LYS Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 63 ARG Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 175 ASP Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 203 THR Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 253 SER Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 263 LEU Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain N residue 418 VAL Chi-restraints excluded: chain N residue 422 VAL Chi-restraints excluded: chain N residue 431 PHE Chi-restraints excluded: chain N residue 466 LEU Chi-restraints excluded: chain N residue 470 PHE Chi-restraints excluded: chain N residue 519 LEU Chi-restraints excluded: chain N residue 529 TYR Chi-restraints excluded: chain N residue 534 VAL Chi-restraints excluded: chain N residue 537 LEU Chi-restraints excluded: chain N residue 540 LEU Chi-restraints excluded: chain N residue 553 THR Chi-restraints excluded: chain N residue 573 ILE Chi-restraints excluded: chain N residue 592 LEU Chi-restraints excluded: chain N residue 608 ILE Chi-restraints excluded: chain N residue 609 LEU Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 52 PHE Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 56 LEU Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain S residue 17 VAL Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 67 ILE Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 70 LEU Chi-restraints excluded: chain T residue 72 ILE Chi-restraints excluded: chain U residue 10 LEU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 21 LEU Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain V residue 58 PHE Chi-restraints excluded: chain V residue 60 LEU Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain V residue 72 ILE Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 30 THR Chi-restraints excluded: chain W residue 51 ASN Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain X residue 19 MET Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain Y residue 19 MET Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Y residue 80 LEU Chi-restraints excluded: chain Z residue 17 VAL Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain Z residue 67 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 170 optimal weight: 10.0000 chunk 74 optimal weight: 0.0770 chunk 571 optimal weight: 10.0000 chunk 465 optimal weight: 9.9990 chunk 126 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 chunk 73 optimal weight: 8.9990 chunk 527 optimal weight: 2.9990 chunk 188 optimal weight: 20.0000 chunk 429 optimal weight: 6.9990 chunk 561 optimal weight: 6.9990 overall best weight: 3.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS C 498 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN ** K 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 ASN M 91 ASN M 94 HIS M 97 GLN M 126 GLN N 386 ASN N 554 GLN ** N 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 51 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 = 0.3812 r_free = 0.3812 target = 0.145971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.107706 restraints weight = 67401.984| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.20 r_work: 0.3170 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 45669 Z= 0.164 Angle : 0.715 13.404 61839 Z= 0.348 Chirality : 0.045 0.207 7079 Planarity : 0.005 0.087 8046 Dihedral : 5.376 81.420 6447 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.82 % Favored : 94.14 % Rotamer: Outliers : 5.07 % Allowed : 19.00 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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 are not related in a simple way. whole: -0.43 (0.11), residues: 5822 helix: 0.93 (0.09), residues: 3148 sheet: -1.39 (0.22), residues: 558 loop : -1.83 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG J 32 TYR 0.053 0.001 TYR N 424 PHE 0.020 0.001 PHE B 361 TRP 0.023 0.001 TRP L 100 HIS 0.008 0.001 HIS H 84 Details of bonding type rmsd covalent geometry : bond 0.00382 (45668) covalent geometry : angle 0.71471 (61837) SS BOND : bond 0.00079 ( 1) SS BOND : angle 0.25122 ( 2) hydrogen bonds : bond 0.04303 ( 2662) hydrogen bonds : angle 4.56165 ( 8004) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11644 Ramachandran restraints generated. 5822 Oldfield, 0 Emsley, 5822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11644 Ramachandran restraints generated. 5822 Oldfield, 0 Emsley, 5822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1165 residues out of total 4601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 935 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO L 146 " (corrupted residue). Skipping it. Corrupt residue: chain: L residue: PRO 146 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.9028 (t0) cc_final: 0.8758 (t0) REVERT: A 400 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8991 (tt) REVERT: A 412 SER cc_start: 0.9060 (m) cc_final: 0.8802 (t) REVERT: A 466 GLU cc_start: 0.8068 (tt0) cc_final: 0.7812 (tt0) REVERT: A 469 GLN cc_start: 0.8074 (mt0) cc_final: 0.7637 (pp30) REVERT: A 489 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8713 (tt) REVERT: A 520 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8617 (mm) REVERT: B 128 GLU cc_start: 0.8726 (tt0) cc_final: 0.8407 (tt0) REVERT: B 130 ARG cc_start: 0.8228 (pmm-80) cc_final: 0.7426 (ptm-80) REVERT: B 166 TYR cc_start: 0.8249 (m-10) cc_final: 0.7865 (m-10) REVERT: B 287 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8726 (mt) REVERT: B 481 ARG cc_start: 0.7610 (ttt180) cc_final: 0.7089 (ttm110) REVERT: B 542 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.6623 (tt) REVERT: C 147 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8827 (pt) REVERT: C 156 ARG cc_start: 0.8417 (mtp-110) cc_final: 0.8031 (mtp-110) REVERT: C 341 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8170 (tt) REVERT: C 393 GLU cc_start: 0.8295 (tt0) cc_final: 0.7920 (tt0) REVERT: C 441 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8243 (mp0) REVERT: C 450 LEU cc_start: 0.9166 (tp) cc_final: 0.8896 (tp) REVERT: C 502 GLU cc_start: 0.8541 (tp30) cc_final: 0.8188 (pt0) REVERT: C 525 GLU cc_start: 0.8540 (tt0) cc_final: 0.8017 (mt-10) REVERT: D 26 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.7730 (t70) REVERT: D 136 SER cc_start: 0.9306 (t) cc_final: 0.9053 (p) REVERT: D 185 GLU cc_start: 0.7814 (pp20) cc_final: 0.7489 (pm20) REVERT: D 283 TYR cc_start: 0.9208 (m-80) cc_final: 0.9008 (m-80) REVERT: D 412 LEU cc_start: 0.9067 (tt) cc_final: 0.8866 (tp) REVERT: E 96 ILE cc_start: 0.8815 (mm) cc_final: 0.8552 (pt) REVERT: E 269 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8353 (tm-30) REVERT: E 342 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8468 (pm20) REVERT: E 409 ARG cc_start: 0.8279 (ttm110) cc_final: 0.7831 (mtm-85) REVERT: E 413 GLN cc_start: 0.8327 (mt0) cc_final: 0.8094 (mp10) REVERT: F 7 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8069 (mp0) REVERT: F 57 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.9002 (mp) REVERT: F 77 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7843 (mm-30) REVERT: F 79 VAL cc_start: 0.9015 (m) cc_final: 0.8473 (p) REVERT: F 259 ASP cc_start: 0.8560 (p0) cc_final: 0.7856 (p0) REVERT: F 275 GLU cc_start: 0.8535 (mt-10) cc_final: 0.7964 (tm-30) REVERT: F 361 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8816 (pp) REVERT: G 59 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7205 (tp30) REVERT: G 144 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: H 48 ASP cc_start: 0.7456 (t70) cc_final: 0.6545 (t0) REVERT: I 31 LYS cc_start: 0.8814 (ptpp) cc_final: 0.8598 (ptpp) REVERT: I 50 ARG cc_start: 0.8815 (ttp80) cc_final: 0.8515 (ttp80) REVERT: I 63 GLU cc_start: 0.8800 (pp20) cc_final: 0.8559 (pp20) REVERT: I 73 TYR cc_start: 0.8549 (t80) cc_final: 0.7855 (t80) REVERT: I 74 ARG cc_start: 0.8302 (mmp80) cc_final: 0.7926 (mmp80) REVERT: I 76 ARG cc_start: 0.8314 (ttp80) cc_final: 0.8019 (ttp80) REVERT: I 78 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8283 (ppp-140) REVERT: I 85 LEU cc_start: 0.7877 (mt) cc_final: 0.7576 (pp) REVERT: I 97 LYS cc_start: 0.8157 (mmpt) cc_final: 0.7864 (mmmt) REVERT: J 32 ARG cc_start: 0.7786 (ttp80) cc_final: 0.7577 (tmm160) REVERT: J 36 GLU cc_start: 0.8395 (pp20) cc_final: 0.8147 (pp20) REVERT: J 49 LEU cc_start: 0.9265 (mt) cc_final: 0.8946 (tt) REVERT: J 52 GLN cc_start: 0.9464 (pp30) cc_final: 0.8941 (pp30) REVERT: J 54 ARG cc_start: 0.9349 (mmp80) cc_final: 0.8911 (mmp80) REVERT: J 110 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8782 (tm-30) REVERT: J 113 GLU cc_start: 0.8029 (mp0) cc_final: 0.7749 (mp0) REVERT: J 175 TRP cc_start: 0.6645 (t-100) cc_final: 0.6071 (t-100) REVERT: K 43 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8236 (tm-30) REVERT: K 78 ARG cc_start: 0.7858 (tpt90) cc_final: 0.7559 (tpt90) REVERT: K 82 GLU cc_start: 0.8159 (tp30) cc_final: 0.7817 (mm-30) REVERT: K 87 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7651 (ttp80) REVERT: K 115 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8128 (mm) REVERT: L 35 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8600 (tm-30) REVERT: L 74 GLN cc_start: 0.8608 (tt0) cc_final: 0.8373 (tt0) REVERT: L 109 LEU cc_start: 0.7854 (tt) cc_final: 0.7337 (pp) REVERT: L 143 GLN cc_start: 0.7435 (tm-30) cc_final: 0.6623 (tm-30) REVERT: M 52 GLN cc_start: 0.8426 (tm130) cc_final: 0.8072 (mm110) REVERT: M 59 ARG cc_start: 0.8369 (tmt-80) cc_final: 0.7804 (tmt-80) REVERT: M 79 GLU cc_start: 0.8397 (tp30) cc_final: 0.7898 (tp30) REVERT: M 138 GLN cc_start: 0.8890 (tm130) cc_final: 0.8478 (tm-30) REVERT: M 207 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8312 (mm) REVERT: M 262 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7065 (tm-30) REVERT: M 303 LEU cc_start: 0.7535 (mm) cc_final: 0.7242 (mm) REVERT: N 5 MET cc_start: 0.7363 (tpt) cc_final: 0.7125 (tpp) REVERT: N 19 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7335 (tm-30) REVERT: N 21 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8586 (tt) REVERT: N 57 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8179 (mt-10) REVERT: N 99 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8182 (tm-30) REVERT: N 124 ARG cc_start: 0.8920 (tpm170) cc_final: 0.8490 (ttt180) REVERT: N 267 GLU cc_start: 0.8805 (pt0) cc_final: 0.7833 (pp20) REVERT: N 268 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8327 (tp30) REVERT: N 431 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.7063 (t80) REVERT: N 492 MET cc_start: 0.7389 (tpt) cc_final: 0.7126 (tpt) REVERT: N 505 LEU cc_start: 0.9206 (tp) cc_final: 0.8891 (tt) REVERT: N 528 MET cc_start: 0.7399 (tmt) cc_final: 0.7053 (tmm) REVERT: N 541 MET cc_start: 0.7795 (ttm) cc_final: 0.7143 (ttm) REVERT: N 547 MET cc_start: 0.8229 (mtm) cc_final: 0.7943 (ttm) REVERT: N 559 LEU cc_start: 0.9140 (tt) cc_final: 0.8882 (mp) REVERT: O 51 ASN cc_start: 0.7903 (m110) cc_final: 0.7554 (m-40) REVERT: O 61 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7963 (tm) REVERT: P 25 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6989 (mp) REVERT: R 10 LEU cc_start: 0.7957 (tp) cc_final: 0.7630 (tp) REVERT: T 52 PHE cc_start: 0.7931 (t80) cc_final: 0.7438 (t80) REVERT: T 67 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8088 (tp) REVERT: U 14 LEU cc_start: 0.8307 (tp) cc_final: 0.8001 (tp) REVERT: V 28 LEU cc_start: 0.8439 (tp) cc_final: 0.8178 (tp) REVERT: Y 80 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6516 (tt) outliers start: 230 outliers final: 166 residues processed: 1077 average time/residue: 0.2693 time to fit residues: 469.8305 Evaluate side-chains 1078 residues out of total 4601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 891 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 78 ARG Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 63 ARG Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 203 THR Chi-restraints excluded: chain M residue 207 LEU Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 263 LEU Chi-restraints excluded: chain N residue 407 VAL Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain N residue 422 VAL Chi-restraints excluded: chain N residue 431 PHE Chi-restraints excluded: chain N residue 470 PHE Chi-restraints excluded: chain N residue 519 LEU Chi-restraints excluded: chain N residue 529 TYR Chi-restraints excluded: chain N residue 534 VAL Chi-restraints excluded: chain N residue 537 LEU Chi-restraints excluded: chain N residue 540 LEU Chi-restraints excluded: chain N residue 553 THR Chi-restraints excluded: chain N residue 573 ILE Chi-restraints excluded: chain N residue 592 LEU Chi-restraints excluded: chain N residue 599 LEU Chi-restraints excluded: chain N residue 609 LEU Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 52 PHE Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 56 LEU Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain S residue 17 VAL Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 67 ILE Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 70 LEU Chi-restraints excluded: chain U residue 10 LEU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 21 LEU Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 70 LEU Chi-restraints excluded: chain V residue 58 PHE Chi-restraints excluded: chain V residue 60 LEU Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 30 THR Chi-restraints excluded: chain W residue 51 ASN Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 19 MET Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain Y residue 19 MET Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Y residue 80 LEU Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain Z residue 67 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 170 optimal weight: 9.9990 chunk 278 optimal weight: 4.9990 chunk 275 optimal weight: 20.0000 chunk 500 optimal weight: 9.9990 chunk 311 optimal weight: 7.9990 chunk 508 optimal weight: 5.9990 chunk 261 optimal weight: 10.0000 chunk 553 optimal weight: 9.9990 chunk 524 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN C 283 HIS D 375 HIS ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN ** F 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN ** K 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 91 ASN M 94 HIS M 97 GLN ** N 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 386 ASN N 554 GLN ** N 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 GLN Y 77 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.143002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.104651 restraints weight = 68329.768| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.19 r_work: 0.3130 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 45669 Z= 0.249 Angle : 0.775 13.085 61839 Z= 0.382 Chirality : 0.048 0.307 7079 Planarity : 0.005 0.079 8046 Dihedral : 5.485 82.140 6447 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.48 % Favored : 93.49 % Rotamer: Outliers : 5.00 % Allowed : 19.51 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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 are not related in a simple way. whole: -0.52 (0.11), residues: 5822 helix: 0.85 (0.09), residues: 3160 sheet: -1.44 (0.22), residues: 556 loop : -1.87 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 47 TYR 0.053 0.002 TYR N 424 PHE 0.025 0.002 PHE A 406 TRP 0.018 0.001 TRP L 100 HIS 0.008 0.001 HIS H 84 Details of bonding type rmsd covalent geometry : bond 0.00597 (45668) covalent geometry : angle 0.77500 (61837) SS BOND : bond 0.00010 ( 1) SS BOND : angle 0.48905 ( 2) hydrogen bonds : bond 0.04640 ( 2662) hydrogen bonds : angle 4.69865 ( 8004) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11644 Ramachandran restraints generated. 5822 Oldfield, 0 Emsley, 5822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11644 Ramachandran restraints generated. 5822 Oldfield, 0 Emsley, 5822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1110 residues out of total 4601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 883 time to evaluate : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO L 146 " (corrupted residue). Skipping it. Corrupt residue: chain: L residue: PRO 146 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.9050 (t0) cc_final: 0.8757 (t0) REVERT: A 400 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9070 (tt) REVERT: A 412 SER cc_start: 0.9074 (m) cc_final: 0.8822 (t) REVERT: A 466 GLU cc_start: 0.8048 (tt0) cc_final: 0.7779 (tt0) REVERT: A 469 GLN cc_start: 0.8192 (mt0) cc_final: 0.7736 (pp30) REVERT: A 520 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8670 (mm) REVERT: A 575 LYS cc_start: 0.8560 (tptp) cc_final: 0.8347 (tptm) REVERT: B 130 ARG cc_start: 0.8249 (pmm-80) cc_final: 0.7464 (ptm-80) REVERT: B 166 TYR cc_start: 0.8337 (m-10) cc_final: 0.7910 (m-10) REVERT: B 287 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8720 (tt) REVERT: B 481 ARG cc_start: 0.7658 (ttt180) cc_final: 0.7109 (ttm110) REVERT: B 542 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.6669 (tt) REVERT: C 147 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8895 (pt) REVERT: C 341 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8396 (tt) REVERT: C 393 GLU cc_start: 0.8335 (tt0) cc_final: 0.7964 (tt0) REVERT: C 450 LEU cc_start: 0.9197 (tp) cc_final: 0.8922 (tp) REVERT: C 502 GLU cc_start: 0.8576 (tp30) cc_final: 0.8207 (pt0) REVERT: C 525 GLU cc_start: 0.8562 (tt0) cc_final: 0.8075 (mt-10) REVERT: D 136 SER cc_start: 0.9375 (t) cc_final: 0.9077 (p) REVERT: D 283 TYR cc_start: 0.9243 (m-80) cc_final: 0.7978 (m-80) REVERT: E 96 ILE cc_start: 0.8705 (mm) cc_final: 0.8499 (pt) REVERT: E 342 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8452 (pm20) REVERT: E 409 ARG cc_start: 0.8336 (ttm110) cc_final: 0.7866 (mtm-85) REVERT: E 413 GLN cc_start: 0.8360 (mt0) cc_final: 0.8115 (mp10) REVERT: F 57 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.8989 (mp) REVERT: F 77 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7846 (mm-30) REVERT: F 259 ASP cc_start: 0.8590 (p0) cc_final: 0.7884 (p0) REVERT: G 59 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7160 (tp30) REVERT: G 144 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: H 36 LEU cc_start: 0.8502 (mt) cc_final: 0.8285 (mt) REVERT: I 47 ARG cc_start: 0.8746 (mmm160) cc_final: 0.8277 (mmm160) REVERT: I 73 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.8259 (t80) REVERT: I 85 LEU cc_start: 0.7902 (mt) cc_final: 0.7602 (pp) REVERT: I 97 LYS cc_start: 0.8171 (mmpt) cc_final: 0.7839 (mmmt) REVERT: J 54 ARG cc_start: 0.9387 (mmp80) cc_final: 0.9007 (mmp80) REVERT: J 81 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8597 (pp20) REVERT: J 110 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8866 (tm-30) REVERT: J 175 TRP cc_start: 0.6919 (t-100) cc_final: 0.6302 (t-100) REVERT: K 43 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8259 (tm-30) REVERT: K 87 ARG cc_start: 0.7981 (ttp80) cc_final: 0.7661 (ttp80) REVERT: K 115 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8109 (mm) REVERT: L 22 GLU cc_start: 0.9535 (pt0) cc_final: 0.9306 (pp20) REVERT: L 31 LYS cc_start: 0.9335 (ptpp) cc_final: 0.8975 (ptpp) REVERT: L 35 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8655 (tm-30) REVERT: L 74 GLN cc_start: 0.8582 (tt0) cc_final: 0.8336 (tt0) REVERT: L 143 GLN cc_start: 0.7333 (tm-30) cc_final: 0.6543 (tm-30) REVERT: M 59 ARG cc_start: 0.8395 (tmt-80) cc_final: 0.7742 (tmt-80) REVERT: M 79 GLU cc_start: 0.8487 (tp30) cc_final: 0.7998 (tp30) REVERT: M 138 GLN cc_start: 0.8922 (tm130) cc_final: 0.8502 (tm-30) REVERT: M 219 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7653 (pp) REVERT: M 262 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7128 (tm-30) REVERT: M 303 LEU cc_start: 0.7572 (mm) cc_final: 0.7267 (mm) REVERT: N 5 MET cc_start: 0.7459 (tpt) cc_final: 0.7239 (tpp) REVERT: N 19 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7415 (tm-30) REVERT: N 21 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8607 (tt) REVERT: N 57 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8194 (mt-10) REVERT: N 99 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8221 (tm-30) REVERT: N 110 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8140 (mp0) REVERT: N 267 GLU cc_start: 0.8837 (pt0) cc_final: 0.7890 (pp20) REVERT: N 268 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8347 (tp30) REVERT: N 431 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.7058 (t80) REVERT: N 492 MET cc_start: 0.7413 (tpt) cc_final: 0.7120 (tpt) REVERT: N 505 LEU cc_start: 0.9213 (tp) cc_final: 0.8893 (tt) REVERT: N 528 MET cc_start: 0.7529 (tmt) cc_final: 0.7117 (tmm) REVERT: N 541 MET cc_start: 0.7889 (ttm) cc_final: 0.7239 (ttm) REVERT: N 547 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7981 (ttm) REVERT: N 649 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7513 (ptt-90) REVERT: O 10 LEU cc_start: 0.6164 (tp) cc_final: 0.5961 (tp) REVERT: O 51 ASN cc_start: 0.7902 (m110) cc_final: 0.7567 (m-40) REVERT: O 61 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8039 (tm) REVERT: P 14 LEU cc_start: 0.8054 (tp) cc_final: 0.7813 (tp) REVERT: P 25 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7068 (mp) REVERT: R 10 LEU cc_start: 0.7873 (tp) cc_final: 0.7564 (tp) REVERT: T 11 ASP cc_start: 0.8124 (t0) cc_final: 0.7579 (m-30) REVERT: T 52 PHE cc_start: 0.7948 (t80) cc_final: 0.7455 (t80) REVERT: U 14 LEU cc_start: 0.8395 (tp) cc_final: 0.8082 (tp) REVERT: V 28 LEU cc_start: 0.8434 (tp) cc_final: 0.8150 (tp) outliers start: 227 outliers final: 182 residues processed: 1022 average time/residue: 0.2646 time to fit residues: 439.9308 Evaluate side-chains 1060 residues out of total 4601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 861 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 466 LYS Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 73 TYR Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 36 ARG Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 97 LYS Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 97 GLN Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 203 THR Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 253 SER Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 263 LEU Chi-restraints excluded: chain N residue 407 VAL Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain N residue 418 VAL Chi-restraints excluded: chain N residue 422 VAL Chi-restraints excluded: chain N residue 431 PHE Chi-restraints excluded: chain N residue 470 PHE Chi-restraints excluded: chain N residue 519 LEU Chi-restraints excluded: chain N residue 524 LEU Chi-restraints excluded: chain N residue 529 TYR Chi-restraints excluded: chain N residue 534 VAL Chi-restraints excluded: chain N residue 537 LEU Chi-restraints excluded: chain N residue 540 LEU Chi-restraints excluded: chain N residue 547 MET Chi-restraints excluded: chain N residue 553 THR Chi-restraints excluded: chain N residue 573 ILE Chi-restraints excluded: chain N residue 592 LEU Chi-restraints excluded: chain N residue 599 LEU Chi-restraints excluded: chain N residue 609 LEU Chi-restraints excluded: chain N residue 649 ARG Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 37 ILE Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 56 LEU Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain S residue 17 VAL Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 67 ILE Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 70 LEU Chi-restraints excluded: chain U residue 10 LEU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 21 LEU Chi-restraints excluded: chain U residue 70 LEU Chi-restraints excluded: chain V residue 58 PHE Chi-restraints excluded: chain V residue 60 LEU Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 30 THR Chi-restraints excluded: chain W residue 51 ASN Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 19 MET Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain Y residue 19 MET Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Z residue 17 VAL Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain Z residue 67 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 197 optimal weight: 4.9990 chunk 363 optimal weight: 7.9990 chunk 206 optimal weight: 0.9980 chunk 322 optimal weight: 0.9980 chunk 296 optimal weight: 1.9990 chunk 390 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 356 optimal weight: 40.0000 chunk 245 optimal weight: 6.9990 chunk 478 optimal weight: 30.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN ** K 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 91 ASN ** M 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 386 ASN N 554 GLN ** N 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 GLN Y 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.146860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.108639 restraints weight = 67285.066| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.20 r_work: 0.3182 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 45669 Z= 0.149 Angle : 0.728 14.795 61839 Z= 0.355 Chirality : 0.045 0.317 7079 Planarity : 0.004 0.070 8046 Dihedral : 5.310 81.792 6447 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.65 % Favored : 94.31 % Rotamer: Outliers : 4.17 % Allowed : 20.68 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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 are not related in a simple way. whole: -0.34 (0.11), residues: 5822 helix: 0.98 (0.09), residues: 3152 sheet: -1.35 (0.22), residues: 551 loop : -1.73 (0.14), residues: 2119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG I 74 TYR 0.044 0.001 TYR N 424 PHE 0.021 0.001 PHE M 230 TRP 0.022 0.001 TRP L 100 HIS 0.008 0.001 HIS H 84 Details of bonding type rmsd covalent geometry : bond 0.00340 (45668) covalent geometry : angle 0.72790 (61837) SS BOND : bond 0.00128 ( 1) SS BOND : angle 0.15073 ( 2) hydrogen bonds : bond 0.04284 ( 2662) hydrogen bonds : angle 4.56402 ( 8004) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11644 Ramachandran restraints generated. 5822 Oldfield, 0 Emsley, 5822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11644 Ramachandran restraints generated. 5822 Oldfield, 0 Emsley, 5822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1121 residues out of total 4601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 932 time to evaluate : 1.438 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 TARDY: cannot create tardy model for: "PRO L 146 " (corrupted residue). Skipping it. Corrupt residue: chain: L residue: PRO 146 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9225 (ttmm) cc_final: 0.8707 (tttt) REVERT: A 54 ASP cc_start: 0.9053 (t0) cc_final: 0.8796 (t0) REVERT: A 400 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8971 (tt) REVERT: A 412 SER cc_start: 0.9052 (m) cc_final: 0.8807 (t) REVERT: A 466 GLU cc_start: 0.8138 (tt0) cc_final: 0.7892 (tt0) REVERT: A 469 GLN cc_start: 0.8067 (mt0) cc_final: 0.7634 (pp30) REVERT: A 489 ILE cc_start: 0.9041 (tt) cc_final: 0.8760 (tp) REVERT: A 520 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8607 (mm) REVERT: B 43 ASP cc_start: 0.7880 (t0) cc_final: 0.7633 (m-30) REVERT: B 45 ASP cc_start: 0.8979 (t70) cc_final: 0.8624 (t0) REVERT: B 130 ARG cc_start: 0.8236 (pmm-80) cc_final: 0.7407 (ptm-80) REVERT: B 166 TYR cc_start: 0.8306 (m-10) cc_final: 0.7931 (m-10) REVERT: B 361 PHE cc_start: 0.8884 (t80) cc_final: 0.8678 (t80) REVERT: B 481 ARG cc_start: 0.7587 (ttt180) cc_final: 0.7056 (ttm110) REVERT: B 542 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.6697 (tt) REVERT: C 1 MET cc_start: 0.7024 (tpp) cc_final: 0.6806 (tpp) REVERT: C 147 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8761 (pt) REVERT: C 156 ARG cc_start: 0.8405 (mtp-110) cc_final: 0.7997 (mtp-110) REVERT: C 341 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8179 (tt) REVERT: C 393 GLU cc_start: 0.8312 (tt0) cc_final: 0.7955 (tt0) REVERT: C 441 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8232 (mp0) REVERT: C 502 GLU cc_start: 0.8484 (tp30) cc_final: 0.8169 (pt0) REVERT: C 520 LEU cc_start: 0.9257 (mt) cc_final: 0.8789 (mt) REVERT: C 525 GLU cc_start: 0.8547 (tt0) cc_final: 0.7902 (mt-10) REVERT: D 136 SER cc_start: 0.9296 (t) cc_final: 0.9047 (p) REVERT: D 185 GLU cc_start: 0.7811 (pp20) cc_final: 0.7462 (pm20) REVERT: D 283 TYR cc_start: 0.9191 (m-80) cc_final: 0.8975 (m-80) REVERT: D 349 TYR cc_start: 0.8585 (t80) cc_final: 0.7914 (t80) REVERT: D 466 LYS cc_start: 0.8339 (mtmt) cc_final: 0.7997 (ptpp) REVERT: E 96 ILE cc_start: 0.8773 (mm) cc_final: 0.8527 (pt) REVERT: E 194 MET cc_start: 0.8561 (mtm) cc_final: 0.7449 (mtm) REVERT: E 210 ARG cc_start: 0.8676 (ttp80) cc_final: 0.8121 (ptt90) REVERT: E 269 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8371 (tm-30) REVERT: E 342 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8427 (pm20) REVERT: E 413 GLN cc_start: 0.8329 (mt0) cc_final: 0.8083 (mp10) REVERT: F 79 VAL cc_start: 0.9001 (m) cc_final: 0.8476 (p) REVERT: F 259 ASP cc_start: 0.8556 (p0) cc_final: 0.7835 (p0) REVERT: F 275 GLU cc_start: 0.8496 (mt-10) cc_final: 0.7991 (tm-30) REVERT: G 55 GLN cc_start: 0.8384 (tm-30) cc_final: 0.7839 (tp40) REVERT: G 59 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7159 (tp30) REVERT: G 144 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7867 (tt0) REVERT: G 158 THR cc_start: 0.8695 (m) cc_final: 0.8367 (m) REVERT: I 47 ARG cc_start: 0.8738 (mmm160) cc_final: 0.8374 (mmm160) REVERT: I 74 ARG cc_start: 0.8349 (mmp80) cc_final: 0.8065 (mmp80) REVERT: I 85 LEU cc_start: 0.7786 (mt) cc_final: 0.7478 (pp) REVERT: I 97 LYS cc_start: 0.8131 (mmpt) cc_final: 0.7772 (mmmt) REVERT: J 59 ARG cc_start: 0.9045 (ttp80) cc_final: 0.8796 (ttp80) REVERT: J 81 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8575 (pp20) REVERT: J 110 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8773 (tm-30) REVERT: J 113 GLU cc_start: 0.7878 (mp0) cc_final: 0.7631 (mp0) REVERT: K 43 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8274 (tm-30) REVERT: K 87 ARG cc_start: 0.7998 (ttp80) cc_final: 0.7679 (ttp80) REVERT: K 115 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8143 (mm) REVERT: L 35 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8583 (tm-30) REVERT: L 39 LYS cc_start: 0.9157 (pttp) cc_final: 0.8954 (pttp) REVERT: L 74 GLN cc_start: 0.8588 (tt0) cc_final: 0.8352 (tt0) REVERT: L 110 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8129 (tm-30) REVERT: L 143 GLN cc_start: 0.7451 (tm-30) cc_final: 0.6648 (tm-30) REVERT: L 181 LYS cc_start: 0.8201 (mtpp) cc_final: 0.7876 (mtmm) REVERT: M 109 PHE cc_start: 0.7787 (t80) cc_final: 0.7548 (t80) REVERT: M 138 GLN cc_start: 0.8902 (tm130) cc_final: 0.8535 (tm-30) REVERT: M 174 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7272 (pt0) REVERT: M 194 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8524 (tt) REVERT: M 207 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8333 (mm) REVERT: M 219 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7731 (pp) REVERT: M 262 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7011 (tm-30) REVERT: M 303 LEU cc_start: 0.7460 (mm) cc_final: 0.7236 (mm) REVERT: N 1 MET cc_start: 0.6715 (ttm) cc_final: 0.6453 (ttm) REVERT: N 19 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7233 (tm-30) REVERT: N 21 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8596 (tt) REVERT: N 57 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8166 (mt-10) REVERT: N 99 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8193 (tm-30) REVERT: N 110 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8219 (mt-10) REVERT: N 124 ARG cc_start: 0.8944 (tpm170) cc_final: 0.8470 (ttt180) REVERT: N 267 GLU cc_start: 0.8789 (pt0) cc_final: 0.7780 (pp20) REVERT: N 268 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8294 (tp30) REVERT: N 431 PHE cc_start: 0.7371 (OUTLIER) cc_final: 0.7081 (t80) REVERT: N 505 LEU cc_start: 0.9199 (tp) cc_final: 0.8889 (tt) REVERT: N 528 MET cc_start: 0.7410 (tmt) cc_final: 0.7060 (tmm) REVERT: N 547 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7833 (ttm) REVERT: N 649 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7478 (ptt-90) REVERT: O 51 ASN cc_start: 0.7837 (m110) cc_final: 0.7488 (m-40) REVERT: O 61 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7992 (tm) REVERT: P 25 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7009 (mp) REVERT: T 11 ASP cc_start: 0.8073 (t0) cc_final: 0.7568 (m-30) REVERT: T 52 PHE cc_start: 0.7961 (t80) cc_final: 0.7475 (t80) REVERT: T 67 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8074 (tp) REVERT: U 14 LEU cc_start: 0.8308 (tp) cc_final: 0.7995 (tp) REVERT: V 28 LEU cc_start: 0.8418 (tp) cc_final: 0.8157 (tp) outliers start: 189 outliers final: 148 residues processed: 1053 average time/residue: 0.2401 time to fit residues: 407.1739 Evaluate side-chains 1041 residues out of total 4601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 875 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 97 GLN Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 194 LEU Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 203 THR Chi-restraints excluded: chain M residue 207 LEU Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 253 SER Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 263 LEU Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain N residue 422 VAL Chi-restraints excluded: chain N residue 431 PHE Chi-restraints excluded: chain N residue 451 ILE Chi-restraints excluded: chain N residue 470 PHE Chi-restraints excluded: chain N residue 529 TYR Chi-restraints excluded: chain N residue 537 LEU Chi-restraints excluded: chain N residue 540 LEU Chi-restraints excluded: chain N residue 547 MET Chi-restraints excluded: chain N residue 573 ILE Chi-restraints excluded: chain N residue 592 LEU Chi-restraints excluded: chain N residue 599 LEU Chi-restraints excluded: chain N residue 609 LEU Chi-restraints excluded: chain N residue 649 ARG Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 56 LEU Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain S residue 17 VAL Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 67 ILE Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 70 LEU Chi-restraints excluded: chain U residue 10 LEU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 21 LEU Chi-restraints excluded: chain U residue 70 LEU Chi-restraints excluded: chain V residue 58 PHE Chi-restraints excluded: chain V residue 60 LEU Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 51 ASN Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 19 MET Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain Y residue 19 MET Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Z residue 17 VAL Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain Z residue 67 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 162 optimal weight: 3.9990 chunk 499 optimal weight: 10.0000 chunk 188 optimal weight: 30.0000 chunk 318 optimal weight: 50.0000 chunk 125 optimal weight: 8.9990 chunk 190 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 222 optimal weight: 9.9990 chunk 213 optimal weight: 6.9990 chunk 234 optimal weight: 9.9990 chunk 164 optimal weight: 20.0000 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 HIS M 97 GLN N 323 ASN N 386 ASN N 554 GLN ** N 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 GLN X 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.145946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.107585 restraints weight = 68002.345| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.37 r_work: 0.3157 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 45669 Z= 0.183 Angle : 0.761 15.201 61839 Z= 0.371 Chirality : 0.046 0.311 7079 Planarity : 0.005 0.084 8046 Dihedral : 5.310 82.131 6447 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.98 % Favored : 93.99 % Rotamer: Outliers : 3.97 % Allowed : 20.88 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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 are not related in a simple way. whole: -0.35 (0.11), residues: 5822 helix: 0.95 (0.09), residues: 3160 sheet: -1.32 (0.22), residues: 564 loop : -1.73 (0.14), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG I 76 TYR 0.044 0.001 TYR N 424 PHE 0.023 0.001 PHE M 230 TRP 0.023 0.001 TRP L 100 HIS 0.008 0.001 HIS H 84 Details of bonding type rmsd covalent geometry : bond 0.00433 (45668) covalent geometry : angle 0.76106 (61837) SS BOND : bond 0.00068 ( 1) SS BOND : angle 0.28348 ( 2) hydrogen bonds : bond 0.04368 ( 2662) hydrogen bonds : angle 4.58749 ( 8004) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11644 Ramachandran restraints generated. 5822 Oldfield, 0 Emsley, 5822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11644 Ramachandran restraints generated. 5822 Oldfield, 0 Emsley, 5822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1061 residues out of total 4601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 881 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO L 146 " (corrupted residue). Skipping it. Corrupt residue: chain: L residue: PRO 146 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.9027 (t0) cc_final: 0.8764 (t0) REVERT: A 400 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9008 (tt) REVERT: A 469 GLN cc_start: 0.8122 (mt0) cc_final: 0.7664 (pp30) REVERT: A 489 ILE cc_start: 0.9025 (tt) cc_final: 0.8734 (tp) REVERT: A 520 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8610 (mm) REVERT: A 575 LYS cc_start: 0.8517 (tptp) cc_final: 0.8247 (tptm) REVERT: B 43 ASP cc_start: 0.7989 (t0) cc_final: 0.7745 (m-30) REVERT: B 45 ASP cc_start: 0.8945 (t70) cc_final: 0.8621 (t0) REVERT: B 130 ARG cc_start: 0.8242 (pmm-80) cc_final: 0.7451 (ptm-80) REVERT: B 166 TYR cc_start: 0.8326 (m-10) cc_final: 0.7879 (m-10) REVERT: B 361 PHE cc_start: 0.8928 (t80) cc_final: 0.8702 (t80) REVERT: B 428 TYR cc_start: 0.8774 (p90) cc_final: 0.8257 (p90) REVERT: B 481 ARG cc_start: 0.7584 (ttt180) cc_final: 0.7068 (ttm110) REVERT: B 542 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.6711 (tt) REVERT: C 147 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8847 (pt) REVERT: C 156 ARG cc_start: 0.8363 (mtp-110) cc_final: 0.7945 (mtp-110) REVERT: C 341 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8331 (tt) REVERT: C 393 GLU cc_start: 0.8364 (tt0) cc_final: 0.7985 (tt0) REVERT: C 441 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8233 (mp0) REVERT: C 502 GLU cc_start: 0.8519 (tp30) cc_final: 0.8222 (pt0) REVERT: C 520 LEU cc_start: 0.9241 (mt) cc_final: 0.8749 (mt) REVERT: C 525 GLU cc_start: 0.8563 (tt0) cc_final: 0.7922 (mt-10) REVERT: D 34 ASP cc_start: 0.8503 (m-30) cc_final: 0.8174 (m-30) REVERT: D 136 SER cc_start: 0.9343 (t) cc_final: 0.9055 (p) REVERT: D 185 GLU cc_start: 0.7765 (pp20) cc_final: 0.7442 (pm20) REVERT: D 283 TYR cc_start: 0.9201 (m-80) cc_final: 0.8972 (m-80) REVERT: D 349 TYR cc_start: 0.8627 (t80) cc_final: 0.7949 (t80) REVERT: D 420 ARG cc_start: 0.9188 (ptt-90) cc_final: 0.8971 (ptt180) REVERT: D 466 LYS cc_start: 0.8351 (mtmt) cc_final: 0.8080 (ptpp) REVERT: E 96 ILE cc_start: 0.8733 (mm) cc_final: 0.8473 (pt) REVERT: E 210 ARG cc_start: 0.8679 (ttp80) cc_final: 0.8126 (ptt90) REVERT: E 269 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8421 (tm-30) REVERT: E 342 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8459 (pm20) REVERT: E 409 ARG cc_start: 0.8291 (ttm110) cc_final: 0.7864 (mtm-85) REVERT: E 413 GLN cc_start: 0.8322 (mt0) cc_final: 0.8082 (mp10) REVERT: F 259 ASP cc_start: 0.8583 (p0) cc_final: 0.7873 (p0) REVERT: F 275 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8081 (tm-30) REVERT: G 55 GLN cc_start: 0.8393 (tm-30) cc_final: 0.7878 (tp40) REVERT: G 59 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7197 (tp30) REVERT: G 144 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7832 (tt0) REVERT: I 47 ARG cc_start: 0.8816 (mmm160) cc_final: 0.8371 (mmm160) REVERT: I 63 GLU cc_start: 0.8735 (pp20) cc_final: 0.8421 (pp20) REVERT: I 85 LEU cc_start: 0.7805 (mt) cc_final: 0.7516 (pp) REVERT: I 97 LYS cc_start: 0.8134 (mmpt) cc_final: 0.7760 (mmmt) REVERT: J 47 ARG cc_start: 0.8785 (mtm-85) cc_final: 0.8545 (mtm-85) REVERT: J 59 ARG cc_start: 0.9083 (ttp80) cc_final: 0.8863 (ttp80) REVERT: J 110 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8780 (tm-30) REVERT: J 113 GLU cc_start: 0.7885 (mp0) cc_final: 0.7623 (mp0) REVERT: K 43 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8287 (tm-30) REVERT: K 87 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7610 (ttp80) REVERT: K 115 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8124 (mm) REVERT: L 22 GLU cc_start: 0.9514 (pt0) cc_final: 0.9286 (pp20) REVERT: L 35 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8584 (tm-30) REVERT: L 74 GLN cc_start: 0.8561 (tt0) cc_final: 0.8313 (tt0) REVERT: L 110 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8179 (tm-30) REVERT: L 143 GLN cc_start: 0.7406 (tm-30) cc_final: 0.6588 (tm-30) REVERT: L 181 LYS cc_start: 0.8211 (mtpp) cc_final: 0.7845 (mtmm) REVERT: M 79 GLU cc_start: 0.8494 (tp30) cc_final: 0.7991 (tp30) REVERT: M 109 PHE cc_start: 0.7791 (t80) cc_final: 0.7550 (t80) REVERT: M 138 GLN cc_start: 0.8890 (tm130) cc_final: 0.8535 (tm-30) REVERT: M 174 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7322 (pt0) REVERT: M 194 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8553 (tt) REVERT: M 207 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8331 (mm) REVERT: M 219 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7742 (pp) REVERT: M 262 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7047 (tm-30) REVERT: M 303 LEU cc_start: 0.7675 (mm) cc_final: 0.7385 (mm) REVERT: N 1 MET cc_start: 0.6767 (ttm) cc_final: 0.6481 (ttm) REVERT: N 21 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8596 (tt) REVERT: N 57 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8184 (mt-10) REVERT: N 99 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8193 (tm-30) REVERT: N 105 LYS cc_start: 0.8911 (tptm) cc_final: 0.8319 (pptt) REVERT: N 267 GLU cc_start: 0.8796 (pt0) cc_final: 0.7811 (pp20) REVERT: N 268 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8304 (tp30) REVERT: N 316 ARG cc_start: 0.8346 (ptt90) cc_final: 0.8039 (ptt90) REVERT: N 431 PHE cc_start: 0.7307 (OUTLIER) cc_final: 0.7106 (t80) REVERT: N 492 MET cc_start: 0.7217 (tpt) cc_final: 0.6965 (tpt) REVERT: N 505 LEU cc_start: 0.9200 (tp) cc_final: 0.8880 (tt) REVERT: N 528 MET cc_start: 0.7441 (tmt) cc_final: 0.7060 (tmm) REVERT: N 541 MET cc_start: 0.7905 (ttm) cc_final: 0.7301 (ttm) REVERT: N 547 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7913 (ttm) REVERT: N 649 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7465 (ptt-90) REVERT: O 51 ASN cc_start: 0.7861 (m110) cc_final: 0.7516 (m-40) REVERT: O 61 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8007 (tm) REVERT: P 25 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7102 (mp) REVERT: T 11 ASP cc_start: 0.8034 (t0) cc_final: 0.7566 (m-30) REVERT: T 52 PHE cc_start: 0.7923 (t80) cc_final: 0.7434 (t80) REVERT: U 14 LEU cc_start: 0.8381 (tp) cc_final: 0.8066 (tp) REVERT: V 28 LEU cc_start: 0.8449 (tp) cc_final: 0.8169 (tp) outliers start: 180 outliers final: 154 residues processed: 1003 average time/residue: 0.2293 time to fit residues: 370.4899 Evaluate side-chains 1027 residues out of total 4601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 856 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain M residue 97 GLN Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 194 LEU Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 203 THR Chi-restraints excluded: chain M residue 207 LEU Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 253 SER Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 263 LEU Chi-restraints excluded: chain N residue 323 ASN Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain N residue 422 VAL Chi-restraints excluded: chain N residue 431 PHE Chi-restraints excluded: chain N residue 451 ILE Chi-restraints excluded: chain N residue 470 PHE Chi-restraints excluded: chain N residue 529 TYR Chi-restraints excluded: chain N residue 537 LEU Chi-restraints excluded: chain N residue 540 LEU Chi-restraints excluded: chain N residue 547 MET Chi-restraints excluded: chain N residue 573 ILE Chi-restraints excluded: chain N residue 592 LEU Chi-restraints excluded: chain N residue 599 LEU Chi-restraints excluded: chain N residue 609 LEU Chi-restraints excluded: chain N residue 649 ARG Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 56 LEU Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain S residue 17 VAL Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 67 ILE Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 70 LEU Chi-restraints excluded: chain U residue 10 LEU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 21 LEU Chi-restraints excluded: chain U residue 70 LEU Chi-restraints excluded: chain V residue 58 PHE Chi-restraints excluded: chain V residue 60 LEU Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 51 ASN Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 19 MET Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain Y residue 19 MET Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Z residue 17 VAL Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain Z residue 67 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 505 optimal weight: 9.9990 chunk 549 optimal weight: 20.0000 chunk 387 optimal weight: 0.5980 chunk 544 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 253 optimal weight: 2.9990 chunk 534 optimal weight: 0.9990 chunk 219 optimal weight: 5.9990 chunk 436 optimal weight: 10.0000 chunk 553 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN ** K 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 HIS N 323 ASN N 386 ASN N 554 GLN N 557 HIS ** N 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.147012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.108298 restraints weight = 67827.541| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.23 r_work: 0.3174 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 45669 Z= 0.161 Angle : 0.752 15.570 61839 Z= 0.368 Chirality : 0.046 0.305 7079 Planarity : 0.005 0.080 8046 Dihedral : 5.245 81.799 6447 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.67 % Favored : 94.30 % Rotamer: Outliers : 3.90 % Allowed : 21.10 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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 are not related in a simple way. whole: -0.25 (0.11), residues: 5822 helix: 1.02 (0.10), residues: 3154 sheet: -1.20 (0.22), residues: 536 loop : -1.68 (0.14), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG I 50 TYR 0.040 0.001 TYR N 424 PHE 0.023 0.001 PHE M 230 TRP 0.023 0.001 TRP L 100 HIS 0.007 0.001 HIS H 84 Details of bonding type rmsd covalent geometry : bond 0.00374 (45668) covalent geometry : angle 0.75243 (61837) SS BOND : bond 0.00096 ( 1) SS BOND : angle 0.13671 ( 2) hydrogen bonds : bond 0.04272 ( 2662) hydrogen bonds : angle 4.55369 ( 8004) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14698.82 seconds wall clock time: 250 minutes 5.99 seconds (15005.99 seconds total)