Starting phenix.real_space_refine on Sat Jun 28 21:29:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tmm_25996/06_2025/7tmm_25996.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tmm_25996/06_2025/7tmm_25996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tmm_25996/06_2025/7tmm_25996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tmm_25996/06_2025/7tmm_25996.map" model { file = "/net/cci-nas-00/data/ceres_data/7tmm_25996/06_2025/7tmm_25996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tmm_25996/06_2025/7tmm_25996.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 sd= 0.114 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 85 5.16 5 C 21530 2.51 5 N 6108 2.21 5 O 5988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33713 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 4150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4150 Classifications: {'peptide': 593} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 562} Unresolved non-hydrogen bonds: 429 Unresolved non-hydrogen angles: 527 Unresolved non-hydrogen dihedrals: 336 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 30, 'GLU:plan': 33, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 289 Chain: "B" Number of atoms: 3375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3375 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 331 Unresolved non-hydrogen dihedrals: 209 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 23, 'ASN:plan1': 6, 'ARG:plan': 2, 'ASP:plan': 21} Unresolved non-hydrogen planarities: 191 Chain: "C" Number of atoms: 3985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 3985 Classifications: {'peptide': 592} Incomplete info: {'truncation_to_alanine': 190} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 561} Unresolved non-hydrogen bonds: 596 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 480 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 31, 'PHE:plan': 6, 'GLU:plan': 34, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 390 Chain: "D" Number of atoms: 3266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3266 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 433} Chain breaks: 1 Unresolved non-hydrogen bonds: 335 Unresolved non-hydrogen angles: 413 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 30, 'ASN:plan1': 11, 'ARG:plan': 1, 'ASP:plan': 23} Unresolved non-hydrogen planarities: 243 Chain: "E" Number of atoms: 4006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4006 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 546} Chain breaks: 2 Unresolved non-hydrogen bonds: 465 Unresolved non-hydrogen angles: 572 Unresolved non-hydrogen dihedrals: 368 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 26, 'PHE:plan': 2, 'GLU:plan': 32, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 296 Chain: "F" Number of atoms: 3276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3276 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 433} Chain breaks: 1 Unresolved non-hydrogen bonds: 326 Unresolved non-hydrogen angles: 401 Unresolved non-hydrogen dihedrals: 254 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 21, 'GLU:plan': 28, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 227 Chain: "G" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1322 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 5, 'TRANS': 214} Unresolved non-hydrogen bonds: 443 Unresolved non-hydrogen angles: 538 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 1, 'ASN:plan1': 13, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 27, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 279 Chain: "H" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 578 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 1, 'TRANS': 107} Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 142 Chain: "I" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1313 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'PTRANS': 5, 'TRANS': 214} Unresolved non-hydrogen bonds: 452 Unresolved non-hydrogen angles: 549 Unresolved non-hydrogen dihedrals: 364 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 1, 'ASN:plan1': 13, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 26, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 266 Chain: "J" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 570 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 1, 'TRANS': 106} Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 146 Chain: "K" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1288 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'PTRANS': 5, 'TRANS': 206} Unresolved non-hydrogen bonds: 413 Unresolved non-hydrogen angles: 503 Unresolved non-hydrogen dihedrals: 330 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 1, 'ASN:plan1': 12, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 26, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 249 Chain: "L" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 522 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 1, 'TRANS': 97} Unresolved non-hydrogen bonds: 267 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 139 Chain: "M" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1341 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PTRANS': 3, 'TRANS': 210} Unresolved non-hydrogen bonds: 392 Unresolved non-hydrogen angles: 487 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 12, 'TYR:plan': 3, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 254 Chain: "N" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 610 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 105} Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 366 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 9, 'PHE:plan': 4, 'GLU:plan': 12, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 172 Chain: "O" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 1873 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 294} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 1033 Unresolved non-hydrogen angles: 1316 Unresolved non-hydrogen dihedrals: 839 Unresolved non-hydrogen chiralities: 108 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 5, 'TYR:plan': 9, 'ASN:plan1': 22, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 19, 'GLU:plan': 27, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 552 Chain: "P" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 2211 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 401} Link IDs: {'PTRANS': 9, 'TRANS': 431} Chain breaks: 2 Unresolved non-hydrogen bonds: 1399 Unresolved non-hydrogen angles: 1785 Unresolved non-hydrogen dihedrals: 1131 Unresolved non-hydrogen chiralities: 154 Planarities with less than four sites: {'GLN:plan1': 24, 'ASP:plan': 30, 'TYR:plan': 11, 'ASN:plan1': 24, 'TRP:plan': 5, 'HIS:plan': 10, 'PHE:plan': 15, 'GLU:plan': 32, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 718 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.51, per 1000 atoms: 0.64 Number of scatterers: 33713 At special positions: 0 Unit cell: (131.84, 169.95, 207.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 P 2 15.00 O 5988 8.00 N 6108 7.00 C 21530 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.39 Conformation dependent library (CDL) restraints added in 5.8 seconds 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9820 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 45 sheets defined 56.1% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.50 Creating SS restraints... Processing helix chain 'A' and resid 111 through 120 Processing helix chain 'A' and resid 237 through 244 Processing helix chain 'A' and resid 261 through 273 removed outlier: 3.715A pdb=" N TYR A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 297 Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.766A pdb=" N GLY A 306 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A 307 " --> pdb=" O MET A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 307' Processing helix chain 'A' and resid 327 through 346 removed outlier: 3.915A pdb=" N ALA A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 372 removed outlier: 3.961A pdb=" N TRP A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 380 removed outlier: 3.561A pdb=" N GLY A 379 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A 380 " --> pdb=" O ASP A 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 380' Processing helix chain 'A' and resid 383 through 393 Processing helix chain 'A' and resid 418 through 422 removed outlier: 3.657A pdb=" N GLY A 421 " --> pdb=" O PRO A 418 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP A 422 " --> pdb=" O ALA A 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 418 through 422' Processing helix chain 'A' and resid 425 through 433 Processing helix chain 'A' and resid 442 through 448 removed outlier: 3.677A pdb=" N ARG A 448 " --> pdb=" O LYS A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 477 through 503 removed outlier: 3.980A pdb=" N LEU A 501 " --> pdb=" O GLN A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 507 removed outlier: 3.521A pdb=" N LEU A 507 " --> pdb=" O LYS A 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 504 through 507' Processing helix chain 'A' and resid 508 through 525 Processing helix chain 'A' and resid 539 through 563 Processing helix chain 'A' and resid 566 through 574 removed outlier: 3.782A pdb=" N ASP A 572 " --> pdb=" O SER A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 583 Processing helix chain 'A' and resid 584 through 587 Processing helix chain 'A' and resid 588 through 591 Processing helix chain 'A' and resid 592 through 616 Processing helix chain 'B' and resid 14 through 19 removed outlier: 3.805A pdb=" N GLY B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 179 through 191 Processing helix chain 'B' and resid 218 through 232 removed outlier: 3.830A pdb=" N GLU B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 236 removed outlier: 3.535A pdb=" N GLU B 236 " --> pdb=" O GLY B 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 233 through 236' Processing helix chain 'B' and resid 250 through 271 removed outlier: 4.021A pdb=" N ILE B 254 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Proline residue: B 256 - end of helix Processing helix chain 'B' and resid 280 through 293 removed outlier: 3.515A pdb=" N TYR B 284 " --> pdb=" O ASP B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 317 removed outlier: 3.637A pdb=" N ILE B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 344 through 354 Processing helix chain 'B' and resid 361 through 368 Processing helix chain 'B' and resid 395 through 421 removed outlier: 3.598A pdb=" N ASN B 401 " --> pdb=" O GLY B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 425 Processing helix chain 'B' and resid 426 through 441 Processing helix chain 'B' and resid 453 through 466 Processing helix chain 'B' and resid 477 through 485 Processing helix chain 'C' and resid 111 through 120 Processing helix chain 'C' and resid 237 through 243 Processing helix chain 'C' and resid 261 through 273 Processing helix chain 'C' and resid 286 through 297 Processing helix chain 'C' and resid 325 through 346 removed outlier: 4.751A pdb=" N ILE C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N TYR C 334 " --> pdb=" O GLU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 372 removed outlier: 3.628A pdb=" N TRP C 360 " --> pdb=" O SER C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 380 Processing helix chain 'C' and resid 383 through 393 Processing helix chain 'C' and resid 418 through 422 removed outlier: 3.523A pdb=" N GLY C 421 " --> pdb=" O PRO C 418 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP C 422 " --> pdb=" O ALA C 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 418 through 422' Processing helix chain 'C' and resid 425 through 435 Processing helix chain 'C' and resid 442 through 448 Processing helix chain 'C' and resid 467 through 475 removed outlier: 4.318A pdb=" N SER C 473 " --> pdb=" O LYS C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 502 Processing helix chain 'C' and resid 503 through 507 Processing helix chain 'C' and resid 508 through 525 Processing helix chain 'C' and resid 539 through 563 Processing helix chain 'C' and resid 566 through 574 Processing helix chain 'C' and resid 574 through 584 Processing helix chain 'C' and resid 585 through 587 No H-bonds generated for 'chain 'C' and resid 585 through 587' Processing helix chain 'C' and resid 588 through 591 removed outlier: 3.572A pdb=" N ARG C 591 " --> pdb=" O GLU C 588 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 588 through 591' Processing helix chain 'C' and resid 592 through 614 Processing helix chain 'D' and resid 16 through 21 removed outlier: 3.627A pdb=" N PHE D 20 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN D 21 " --> pdb=" O GLN D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 109 removed outlier: 3.833A pdb=" N LEU D 109 " --> pdb=" O GLU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 142 No H-bonds generated for 'chain 'D' and resid 140 through 142' Processing helix chain 'D' and resid 155 through 160 Processing helix chain 'D' and resid 179 through 191 Processing helix chain 'D' and resid 218 through 233 removed outlier: 3.808A pdb=" N GLU D 230 " --> pdb=" O LYS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 237 removed outlier: 3.730A pdb=" N ARG D 237 " --> pdb=" O SER D 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 234 through 237' Processing helix chain 'D' and resid 248 through 269 Proline residue: D 256 - end of helix Processing helix chain 'D' and resid 280 through 293 Processing helix chain 'D' and resid 307 through 317 removed outlier: 4.039A pdb=" N ILE D 315 " --> pdb=" O ASP D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 341 Processing helix chain 'D' and resid 344 through 354 Processing helix chain 'D' and resid 361 through 368 Processing helix chain 'D' and resid 382 through 387 Processing helix chain 'D' and resid 395 through 421 removed outlier: 3.527A pdb=" N ASN D 401 " --> pdb=" O GLY D 397 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA D 418 " --> pdb=" O ALA D 414 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL D 419 " --> pdb=" O ALA D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 441 removed outlier: 3.669A pdb=" N GLU D 434 " --> pdb=" O LYS D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 466 Processing helix chain 'D' and resid 467 through 468 No H-bonds generated for 'chain 'D' and resid 467 through 468' Processing helix chain 'D' and resid 469 through 473 removed outlier: 3.786A pdb=" N LEU D 473 " --> pdb=" O LYS D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 484 Processing helix chain 'E' and resid 111 through 120 Processing helix chain 'E' and resid 237 through 244 Processing helix chain 'E' and resid 265 through 272 Processing helix chain 'E' and resid 286 through 297 Processing helix chain 'E' and resid 325 through 346 removed outlier: 4.344A pdb=" N ILE E 333 " --> pdb=" O ARG E 329 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 372 removed outlier: 3.573A pdb=" N TRP E 360 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 393 Processing helix chain 'E' and resid 425 through 432 Processing helix chain 'E' and resid 442 through 448 Processing helix chain 'E' and resid 467 through 475 removed outlier: 4.061A pdb=" N SER E 473 " --> pdb=" O LYS E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 503 removed outlier: 3.773A pdb=" N GLN E 497 " --> pdb=" O GLU E 493 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL E 498 " --> pdb=" O GLU E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 525 Processing helix chain 'E' and resid 539 through 563 Processing helix chain 'E' and resid 566 through 574 removed outlier: 4.234A pdb=" N ASP E 572 " --> pdb=" O SER E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 584 Processing helix chain 'E' and resid 585 through 587 No H-bonds generated for 'chain 'E' and resid 585 through 587' Processing helix chain 'E' and resid 588 through 591 Processing helix chain 'E' and resid 592 through 611 Processing helix chain 'F' and resid 105 through 109 removed outlier: 3.790A pdb=" N LEU F 109 " --> pdb=" O GLU F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 142 No H-bonds generated for 'chain 'F' and resid 140 through 142' Processing helix chain 'F' and resid 155 through 160 Processing helix chain 'F' and resid 179 through 190 Processing helix chain 'F' and resid 218 through 232 Processing helix chain 'F' and resid 233 through 236 removed outlier: 3.844A pdb=" N GLU F 236 " --> pdb=" O GLY F 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 233 through 236' Processing helix chain 'F' and resid 250 through 253 Processing helix chain 'F' and resid 254 through 270 Processing helix chain 'F' and resid 280 through 295 Processing helix chain 'F' and resid 300 through 304 Processing helix chain 'F' and resid 305 through 306 No H-bonds generated for 'chain 'F' and resid 305 through 306' Processing helix chain 'F' and resid 307 through 317 Processing helix chain 'F' and resid 338 through 341 Processing helix chain 'F' and resid 344 through 354 Processing helix chain 'F' and resid 361 through 368 Processing helix chain 'F' and resid 382 through 387 Processing helix chain 'F' and resid 395 through 421 Processing helix chain 'F' and resid 426 through 441 Processing helix chain 'F' and resid 453 through 466 Processing helix chain 'F' and resid 467 through 468 No H-bonds generated for 'chain 'F' and resid 467 through 468' Processing helix chain 'F' and resid 469 through 473 removed outlier: 3.822A pdb=" N LEU F 473 " --> pdb=" O LYS F 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 485 removed outlier: 3.976A pdb=" N GLU F 483 " --> pdb=" O LYS F 479 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 49 removed outlier: 3.602A pdb=" N THR G 48 " --> pdb=" O GLU G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 113 removed outlier: 3.745A pdb=" N ALA G 111 " --> pdb=" O LEU G 107 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN G 112 " --> pdb=" O SER G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 133 Proline residue: G 119 - end of helix removed outlier: 3.519A pdb=" N GLN G 122 " --> pdb=" O LYS G 118 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS G 131 " --> pdb=" O GLU G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 164 removed outlier: 3.541A pdb=" N SER G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ASP G 154 " --> pdb=" O GLU G 150 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ASP G 155 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG G 158 " --> pdb=" O ASP G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 223 removed outlier: 3.931A pdb=" N LEU G 215 " --> pdb=" O SER G 211 " (cutoff:3.500A) Proline residue: G 216 - end of helix Processing helix chain 'H' and resid 6 through 103 removed outlier: 3.506A pdb=" N VAL H 65 " --> pdb=" O ASN H 61 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY H 66 " --> pdb=" O ALA H 62 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU H 67 " --> pdb=" O GLY H 63 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ASP H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ASP H 93 " --> pdb=" O LYS H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 111 removed outlier: 3.534A pdb=" N GLU I 30 " --> pdb=" O LYS I 26 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU I 44 " --> pdb=" O ASP I 40 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE I 45 " --> pdb=" O GLN I 41 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER I 108 " --> pdb=" O LYS I 104 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY I 109 " --> pdb=" O GLU I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 131 Proline residue: I 119 - end of helix removed outlier: 3.749A pdb=" N LYS I 131 " --> pdb=" O GLU I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 164 removed outlier: 5.204A pdb=" N ASP I 154 " --> pdb=" O GLU I 150 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ASP I 155 " --> pdb=" O SER I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 214 Processing helix chain 'I' and resid 214 through 224 Processing helix chain 'J' and resid 6 through 63 Processing helix chain 'J' and resid 64 through 104 removed outlier: 3.537A pdb=" N GLY J 75 " --> pdb=" O LYS J 71 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY J 78 " --> pdb=" O ALA J 74 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU J 79 " --> pdb=" O GLY J 75 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ASP J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASP J 93 " --> pdb=" O LYS J 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 113 removed outlier: 3.849A pdb=" N LYS K 83 " --> pdb=" O THR K 79 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU K 86 " --> pdb=" O ASN K 82 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS K 87 " --> pdb=" O LYS K 83 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL K 88 " --> pdb=" O MET K 84 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER K 108 " --> pdb=" O LYS K 104 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN K 113 " --> pdb=" O GLY K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 133 Proline residue: K 119 - end of helix removed outlier: 4.406A pdb=" N VAL K 126 " --> pdb=" O GLN K 122 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LYS K 131 " --> pdb=" O GLU K 127 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU K 132 " --> pdb=" O ALA K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 144 No H-bonds generated for 'chain 'K' and resid 142 through 144' Processing helix chain 'K' and resid 145 through 152 Processing helix chain 'K' and resid 152 through 164 removed outlier: 3.656A pdb=" N GLY K 161 " --> pdb=" O MET K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 214 removed outlier: 3.834A pdb=" N GLU K 212 " --> pdb=" O LYS K 208 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 224 Processing helix chain 'L' and resid 15 through 62 removed outlier: 3.731A pdb=" N ALA L 35 " --> pdb=" O LYS L 31 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS L 36 " --> pdb=" O LEU L 32 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR L 37 " --> pdb=" O LYS L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 103 removed outlier: 5.448A pdb=" N ASP L 92 " --> pdb=" O GLU L 88 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASP L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 11 through 76 removed outlier: 3.601A pdb=" N GLN M 62 " --> pdb=" O GLY M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 86 Processing helix chain 'M' and resid 115 through 118 Processing helix chain 'M' and resid 128 through 176 Processing helix chain 'M' and resid 176 through 217 Processing helix chain 'N' and resid 2 through 6 removed outlier: 3.741A pdb=" N THR N 6 " --> pdb=" O GLU N 3 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 24 Processing helix chain 'N' and resid 46 through 59 Processing helix chain 'N' and resid 71 through 77 removed outlier: 3.767A pdb=" N ASN N 76 " --> pdb=" O HIS N 72 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE N 77 " --> pdb=" O ILE N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 84 Processing helix chain 'N' and resid 102 through 106 Processing helix chain 'N' and resid 108 through 112 Processing helix chain 'O' and resid 29 through 35 Processing helix chain 'O' and resid 57 through 88 Processing helix chain 'O' and resid 89 through 94 removed outlier: 3.633A pdb=" N SER O 93 " --> pdb=" O ASN O 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 99 removed outlier: 3.715A pdb=" N ARG O 98 " --> pdb=" O ASN O 95 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 105 Processing helix chain 'O' and resid 106 through 112 Processing helix chain 'O' and resid 126 through 167 Processing helix chain 'O' and resid 174 through 179 Processing helix chain 'O' and resid 199 through 213 Processing helix chain 'O' and resid 218 through 222 Processing helix chain 'O' and resid 242 through 253 Processing helix chain 'O' and resid 265 through 320 removed outlier: 3.939A pdb=" N VAL O 297 " --> pdb=" O LYS O 293 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE O 300 " --> pdb=" O TYR O 296 " (cutoff:3.500A) Processing helix chain 'O' and resid 333 through 335 No H-bonds generated for 'chain 'O' and resid 333 through 335' Processing helix chain 'O' and resid 336 through 348 Processing helix chain 'O' and resid 349 through 352 Processing helix chain 'P' and resid 5 through 9 Processing helix chain 'P' and resid 10 through 23 Processing helix chain 'P' and resid 26 through 33 removed outlier: 3.642A pdb=" N LEU P 30 " --> pdb=" O ALA P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 37 through 52 Processing helix chain 'P' and resid 73 through 75 No H-bonds generated for 'chain 'P' and resid 73 through 75' Processing helix chain 'P' and resid 76 through 87 removed outlier: 3.537A pdb=" N LEU P 80 " --> pdb=" O THR P 76 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 106 Processing helix chain 'P' and resid 110 through 120 Processing helix chain 'P' and resid 120 through 131 removed outlier: 3.930A pdb=" N LEU P 124 " --> pdb=" O ASP P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 135 through 152 removed outlier: 3.905A pdb=" N GLN P 152 " --> pdb=" O SER P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 166 Processing helix chain 'P' and resid 167 through 176 Processing helix chain 'P' and resid 179 through 194 Processing helix chain 'P' and resid 196 through 206 Processing helix chain 'P' and resid 206 through 223 Proline residue: P 212 - end of helix Processing helix chain 'P' and resid 238 through 256 removed outlier: 4.276A pdb=" N ASN P 256 " --> pdb=" O LEU P 252 " (cutoff:3.500A) Processing helix chain 'P' and resid 256 through 267 Processing helix chain 'P' and resid 267 through 281 removed outlier: 3.718A pdb=" N LYS P 279 " --> pdb=" O LEU P 275 " (cutoff:3.500A) Processing helix chain 'P' and resid 283 through 299 Processing helix chain 'P' and resid 304 through 316 Processing helix chain 'P' and resid 317 through 328 removed outlier: 3.720A pdb=" N THR P 321 " --> pdb=" O ASN P 317 " (cutoff:3.500A) Processing helix chain 'P' and resid 332 through 352 removed outlier: 4.114A pdb=" N GLU P 352 " --> pdb=" O ASN P 348 " (cutoff:3.500A) Processing helix chain 'P' and resid 354 through 366 Processing helix chain 'P' and resid 371 through 376 Processing helix chain 'P' and resid 376 through 383 removed outlier: 3.675A pdb=" N TRP P 380 " --> pdb=" O ASP P 376 " (cutoff:3.500A) Processing helix chain 'P' and resid 383 through 388 removed outlier: 3.610A pdb=" N LYS P 388 " --> pdb=" O ILE P 384 " (cutoff:3.500A) Processing helix chain 'P' and resid 388 through 409 removed outlier: 5.653A pdb=" N ILE P 394 " --> pdb=" O ASP P 390 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE P 395 " --> pdb=" O ASN P 391 " (cutoff:3.500A) Processing helix chain 'P' and resid 413 through 433 Processing helix chain 'P' and resid 436 through 444 removed outlier: 4.429A pdb=" N VAL P 440 " --> pdb=" O GLU P 436 " (cutoff:3.500A) Processing helix chain 'P' and resid 445 through 453 Processing helix chain 'P' and resid 454 through 456 No H-bonds generated for 'chain 'P' and resid 454 through 456' Processing helix chain 'P' and resid 458 through 473 Processing sheet with id=AA1, first strand: chain 'G' and resid 171 through 174 removed outlier: 3.685A pdb=" N VAL G 188 " --> pdb=" O ASN G 201 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU F 26 " --> pdb=" O PHE F 95 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL F 53 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL F 67 " --> pdb=" O GLN F 78 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLN F 78 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU F 69 " --> pdb=" O ILE F 76 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA F 75 " --> pdb=" O LEU F 41 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL A 60 " --> pdb=" O GLN A 71 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLN A 71 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 62 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE A 36 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU A 48 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU A 47 " --> pdb=" O VAL A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 96 Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 105 removed outlier: 3.789A pdb=" N ILE A 279 " --> pdb=" O SER A 351 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU A 225 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105 removed outlier: 3.789A pdb=" N ILE A 279 " --> pdb=" O SER A 351 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 173 removed outlier: 4.074A pdb=" N GLY A 159 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 152 removed outlier: 6.701A pdb=" N GLU A 199 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ILE A 185 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ILE A 197 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 302 removed outlier: 3.896A pdb=" N GLU A 309 " --> pdb=" O THR A 302 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 70 through 71 removed outlier: 5.306A pdb=" N ILE C 27 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLU C 38 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL C 34 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LYS C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ILE C 63 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR C 69 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU B 26 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL I 188 " --> pdb=" O ASN I 201 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 70 through 71 removed outlier: 7.031A pdb=" N LEU C 48 " --> pdb=" O THR C 88 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLU C 47 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU B 26 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL I 188 " --> pdb=" O ASN I 201 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 101 through 104 removed outlier: 3.513A pdb=" N LEU B 132 " --> pdb=" O ILE B 102 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 112 through 113 removed outlier: 7.079A pdb=" N ILE B 210 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N PHE B 241 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE B 212 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ASN B 243 " --> pdb=" O PHE B 212 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ALA B 214 " --> pdb=" O ASN B 243 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N SER B 209 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE B 277 " --> pdb=" O SER B 209 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL B 211 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N THR B 279 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 213 " --> pdb=" O THR B 279 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL B 274 " --> pdb=" O THR B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 144 through 145 removed outlier: 4.146A pdb=" N ARG B 321 " --> pdb=" O ILE B 145 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 334 through 336 removed outlier: 5.970A pdb=" N ILE B 172 " --> pdb=" O LEU B 335 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 93 through 96 Processing sheet with id=AB6, first strand: chain 'C' and resid 104 through 105 removed outlier: 6.334A pdb=" N ILE C 278 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N VAL C 318 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TYR C 280 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ALA C 277 " --> pdb=" O SER C 351 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ILE C 353 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE C 279 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL C 350 " --> pdb=" O SER C 411 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL C 413 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N MET C 352 " --> pdb=" O VAL C 413 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA C 415 " --> pdb=" O MET C 352 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA C 354 " --> pdb=" O ALA C 415 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU C 225 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 104 through 105 removed outlier: 6.334A pdb=" N ILE C 278 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N VAL C 318 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TYR C 280 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ALA C 277 " --> pdb=" O SER C 351 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ILE C 353 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE C 279 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL C 350 " --> pdb=" O SER C 411 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL C 413 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N MET C 352 " --> pdb=" O VAL C 413 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA C 415 " --> pdb=" O MET C 352 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA C 354 " --> pdb=" O ALA C 415 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA C 414 " --> pdb=" O THR C 252 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 170 through 173 removed outlier: 4.205A pdb=" N GLY C 159 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE C 162 " --> pdb=" O GLN C 140 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLN C 140 " --> pdb=" O PHE C 162 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 151 through 152 removed outlier: 6.807A pdb=" N GLU C 199 " --> pdb=" O THR C 183 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 301 through 303 Processing sheet with id=AC2, first strand: chain 'D' and resid 31 through 33 removed outlier: 6.711A pdb=" N ILE D 40 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU D 26 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL K 188 " --> pdb=" O ASN K 201 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 101 through 104 removed outlier: 3.551A pdb=" N ASP D 130 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 112 through 113 removed outlier: 3.630A pdb=" N VAL D 211 " --> pdb=" O LEU D 275 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 144 through 145 removed outlier: 4.036A pdb=" N ARG D 321 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 164 through 165 removed outlier: 4.519A pdb=" N ILE D 164 " --> pdb=" O ILE D 151 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 334 through 336 removed outlier: 6.065A pdb=" N ILE D 172 " --> pdb=" O LEU D 335 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 25 through 31 removed outlier: 6.519A pdb=" N ILE E 36 " --> pdb=" O TYR E 28 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL E 30 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL E 34 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA E 37 " --> pdb=" O ALA E 68 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLN E 71 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N VAL E 60 " --> pdb=" O GLN E 71 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 93 through 96 Processing sheet with id=AD1, first strand: chain 'E' and resid 104 through 105 removed outlier: 6.672A pdb=" N ILE E 278 " --> pdb=" O THR E 316 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL E 318 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TYR E 280 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA E 277 " --> pdb=" O SER E 351 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE E 353 " --> pdb=" O ALA E 277 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE E 279 " --> pdb=" O ILE E 353 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ASP E 355 " --> pdb=" O ILE E 279 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL E 281 " --> pdb=" O ASP E 355 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL E 350 " --> pdb=" O SER E 411 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N VAL E 413 " --> pdb=" O VAL E 350 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N MET E 352 " --> pdb=" O VAL E 413 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL E 410 " --> pdb=" O GLY E 396 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU E 225 " --> pdb=" O VAL E 399 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 170 through 173 removed outlier: 4.089A pdb=" N GLY E 159 " --> pdb=" O ILE E 172 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 151 through 152 removed outlier: 3.531A pdb=" N TRP E 184 " --> pdb=" O GLU E 199 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 232 through 233 removed outlier: 4.470A pdb=" N CYS E 246 " --> pdb=" O LEU E 233 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 301 through 302 Processing sheet with id=AD6, first strand: chain 'E' and resid 437 through 438 Processing sheet with id=AD7, first strand: chain 'F' and resid 101 through 104 Processing sheet with id=AD8, first strand: chain 'F' and resid 112 through 113 removed outlier: 6.693A pdb=" N ILE F 210 " --> pdb=" O SER F 239 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N PHE F 241 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE F 212 " --> pdb=" O PHE F 241 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASN F 243 " --> pdb=" O PHE F 212 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ALA F 214 " --> pdb=" O ASN F 243 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.192A pdb=" N ARG F 321 " --> pdb=" O ILE F 145 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 164 through 165 removed outlier: 4.638A pdb=" N ILE F 164 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY F 192 " --> pdb=" O SER F 152 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 334 through 336 Processing sheet with id=AE3, first strand: chain 'M' and resid 92 through 97 Processing sheet with id=AE4, first strand: chain 'M' and resid 100 through 101 Processing sheet with id=AE5, first strand: chain 'N' and resid 8 through 10 removed outlier: 6.594A pdb=" N ALA N 9 " --> pdb=" O LEU N 68 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ASN N 70 " --> pdb=" O ALA N 9 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 28 through 29 removed outlier: 3.614A pdb=" N GLU N 34 " --> pdb=" O THR N 29 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 46 through 47 Processing sheet with id=AE8, first strand: chain 'O' and resid 191 through 193 Processing sheet with id=AE9, first strand: chain 'O' and resid 223 through 224 2436 hydrogen bonds defined for protein. 7026 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: 17.27 Time building geometry restraints manager: 11.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11478 1.34 - 1.46: 4424 1.46 - 1.57: 18216 1.57 - 1.69: 3 1.69 - 1.81: 153 Bond restraints: 34274 Sorted by residual: bond pdb=" CB MET C 485 " pdb=" CG MET C 485 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.48e+00 bond pdb=" CB VAL B 53 " pdb=" CG1 VAL B 53 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.94e+00 bond pdb=" SD MET F 215 " pdb=" CE MET F 215 " ideal model delta sigma weight residual 1.791 1.757 0.034 2.50e-02 1.60e+03 1.87e+00 bond pdb=" CG PRO A 452 " pdb=" CD PRO A 452 " ideal model delta sigma weight residual 1.512 1.475 0.037 2.70e-02 1.37e+03 1.85e+00 bond pdb=" CB VAL E 410 " pdb=" CG2 VAL E 410 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.74e+00 ... (remaining 34269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 46612 2.10 - 4.19: 460 4.19 - 6.29: 51 6.29 - 8.39: 3 8.39 - 10.49: 4 Bond angle restraints: 47130 Sorted by residual: angle pdb=" C ASP E 377 " pdb=" CA ASP E 377 " pdb=" CB ASP E 377 " ideal model delta sigma weight residual 116.34 110.56 5.78 1.40e+00 5.10e-01 1.70e+01 angle pdb=" CB MET A 547 " pdb=" CG MET A 547 " pdb=" SD MET A 547 " ideal model delta sigma weight residual 112.70 102.63 10.07 3.00e+00 1.11e-01 1.13e+01 angle pdb=" CB MET C 45 " pdb=" CG MET C 45 " pdb=" SD MET C 45 " ideal model delta sigma weight residual 112.70 103.04 9.66 3.00e+00 1.11e-01 1.04e+01 angle pdb=" N TYR A 28 " pdb=" CA TYR A 28 " pdb=" C TYR A 28 " ideal model delta sigma weight residual 114.56 110.58 3.98 1.27e+00 6.20e-01 9.84e+00 angle pdb=" N VAL D 16 " pdb=" CA VAL D 16 " pdb=" C VAL D 16 " ideal model delta sigma weight residual 111.91 109.18 2.73 8.90e-01 1.26e+00 9.43e+00 ... (remaining 47125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.13: 19557 22.13 - 44.26: 665 44.26 - 66.38: 42 66.38 - 88.51: 14 88.51 - 110.64: 4 Dihedral angle restraints: 20282 sinusoidal: 5106 harmonic: 15176 Sorted by residual: dihedral pdb=" O1B ADP A 701 " pdb=" O3A ADP A 701 " pdb=" PB ADP A 701 " pdb=" PA ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 -170.64 110.64 1 2.00e+01 2.50e-03 3.25e+01 dihedral pdb=" CA PHE B 208 " pdb=" C PHE B 208 " pdb=" N SER B 209 " pdb=" CA SER B 209 " ideal model delta harmonic sigma weight residual 180.00 157.52 22.48 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA GLY C 282 " pdb=" C GLY C 282 " pdb=" N CYS C 283 " pdb=" CA CYS C 283 " ideal model delta harmonic sigma weight residual -180.00 -158.57 -21.43 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 20279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3799 0.034 - 0.067: 1470 0.067 - 0.101: 455 0.101 - 0.135: 179 0.135 - 0.169: 15 Chirality restraints: 5918 Sorted by residual: chirality pdb=" CA MET C 485 " pdb=" N MET C 485 " pdb=" C MET C 485 " pdb=" CB MET C 485 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.10e-01 chirality pdb=" CB ILE B 170 " pdb=" CA ILE B 170 " pdb=" CG1 ILE B 170 " pdb=" CG2 ILE B 170 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA ILE E 254 " pdb=" N ILE E 254 " pdb=" C ILE E 254 " pdb=" CB ILE E 254 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 5915 not shown) Planarity restraints: 6176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS G 118 " -0.034 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO G 119 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO G 119 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 119 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 344 " -0.032 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO B 345 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 345 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 345 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 266 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" C LEU F 266 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU F 266 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA F 267 " -0.010 2.00e-02 2.50e+03 ... (remaining 6173 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2383 2.74 - 3.28: 35553 3.28 - 3.82: 58546 3.82 - 4.36: 62533 4.36 - 4.90: 113935 Nonbonded interactions: 272950 Sorted by model distance: nonbonded pdb=" O ILE D 52 " pdb=" OG1 THR D 96 " model vdw 2.195 3.040 nonbonded pdb=" O LEU F 266 " pdb=" OG1 THR F 270 " model vdw 2.207 3.040 nonbonded pdb=" O SER B 163 " pdb=" OG SER B 380 " model vdw 2.207 3.040 nonbonded pdb=" NZ LYS A 262 " pdb=" O1B ADP A 701 " model vdw 2.209 3.120 nonbonded pdb=" O GLU D 296 " pdb=" NE2 GLN M 207 " model vdw 2.218 3.120 ... (remaining 272945 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 24 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )) or resid 56 through 70 or (resid 71 and (name N or nam \ e CA or name C or name O or name CB )) or resid 72 through 109 or (resid 110 and \ (name N or name CA or name C or name O or name CB )) or resid 111 through 112 o \ r (resid 113 through 114 and (name N or name CA or name C or name O or name CB ) \ ) or resid 115 through 116 or (resid 117 through 121 and (name N or name CA or n \ ame C or name O or name CB )) or resid 122 through 129 or (resid 130 and (name N \ or name CA or name C or name O or name CB )) or resid 131 through 135 or (resid \ 136 and (name N or name CA or name C or name O or name CB )) or resid 137 or (r \ esid 138 and (name N or name CA or name C or name O or name CB )) or resid 139 t \ hrough 147 or (resid 148 and (name N or name CA or name C or name O or name CB ) \ ) or resid 149 through 161 or (resid 162 and (name N or name CA or name C or nam \ e O or name CB )) or resid 163 or (resid 164 through 165 and (name N or name CA \ or name C or name O or name CB )) or resid 166 through 167 or (resid 168 through \ 169 and (name N or name CA or name C or name O or name CB )) or resid 170 throu \ gh 180 or (resid 181 and (name N or name CA or name C or name O or name CB )) or \ resid 182 or (resid 183 and (name N or name CA or name C or name O or name CB ) \ ) or resid 184 through 189 or (resid 190 and (name N or name CA or name C or nam \ e O or name CB )) or resid 191 through 196 or (resid 197 and (name N or name CA \ or name C or name O or name CB )) or resid 198 through 201 or (resid 202 through \ 203 and (name N or name CA or name C or name O or name CB )) or (resid 204 thro \ ugh 208 and (name N or name CA or name C or name O or name CB )) or resid 209 or \ (resid 210 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 1 through 217 or (resid 218 and (name N or name CA or name C or name O or name C \ B )) or resid 219 through 223 or (resid 224 through 225 and (name N or name CA o \ r name C or name O or name CB )) or resid 226 through 234 or (resid 235 and (nam \ e N or name CA or name C or name O or name CB )) or resid 236 through 240 or (re \ sid 241 through 242 and (name N or name CA or name C or name O or name CB )) or \ resid 243 through 255 or (resid 264 through 277 and (name N or name CA or name C \ or name O or name CB )) or resid 278 through 289 or (resid 290 through 292 and \ (name N or name CA or name C or name O or name CB )) or resid 293 through 294 or \ (resid 295 through 296 and (name N or name CA or name C or name O or name CB )) \ or resid 297 through 299 or (resid 300 through 305 and (name N or name CA or na \ me C or name O or name CB )) or resid 306 through 310 or (resid 311 and (name N \ or name CA or name C or name O or name CB )) or resid 312 through 314 or (resid \ 315 and (name N or name CA or name C or name O or name CB )) or resid 316 throug \ h 329 or (resid 330 through 332 and (name N or name CA or name C or name O or na \ me CB )) or resid 333 through 361 or (resid 362 through 363 and (name N or name \ CA or name C or name O or name CB )) or resid 364 through 367 or (resid 368 and \ (name N or name CA or name C or name O or name CB )) or resid 369 through 386 or \ (resid 387 and (name N or name CA or name C or name O or name CB )) or resid 38 \ 8 through 389 or (resid 390 and (name N or name CA or name C or name O or name C \ B )) or resid 391 through 406 or (resid 407 and (name N or name CA or name C or \ name O or name CB )) or resid 408 through 416 or (resid 417 and (name N or name \ CA or name C or name O or name CB )) or resid 424 through 440 or (resid 441 thro \ ugh 444 and (name N or name CA or name C or name O or name CB )) or resid 445 th \ rough 446 or (resid 447 through 449 and (name N or name CA or name C or name O o \ r name CB )) or resid 450 or (resid 451 and (name N or name CA or name C or name \ O or name CB )) or resid 452 or (resid 453 and (name N or name CA or name C or \ name O or name CB )) or resid 454 or (resid 455 through 459 and (name N or name \ CA or name C or name O or name CB )) or resid 460 through 479 or (resid 480 and \ (name N or name CA or name C or name O or name CB )) or resid 481 through 482 or \ (resid 483 and (name N or name CA or name C or name O or name CB )) or resid 48 \ 4 through 486 or (resid 487 and (name N or name CA or name C or name O or name C \ B )) or resid 488 through 489 or (resid 490 through 502 and (name N or name CA o \ r name C or name O or name CB )) or (resid 503 through 518 and (name N or name C \ A or name C or name O or name CB )) or resid 519 through 528 or (resid 529 and ( \ name N or name CA or name C or name O or name CB )) or resid 530 or (resid 531 t \ hrough 536 and (name N or name CA or name C or name O or name CB )) or resid 537 \ or (resid 538 and (name N or name CA or name C or name O or name CB )) or resid \ 539 through 551 or (resid 552 and (name N or name CA or name C or name O or nam \ e CB )) or resid 553 through 557 or (resid 558 through 563 and (name N or name C \ A or name C or name O or name CB )) or (resid 564 through 574 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 575 through 580 and (name N or \ name CA or name C or name O or name CB )) or resid 581 or (resid 582 through 584 \ and (name N or name CA or name C or name O or name CB )) or resid 585 through 5 \ 86 or (resid 587 through 588 and (name N or name CA or name C or name O or name \ CB )) or resid 589 through 590 or (resid 591 and (name N or name CA or name C or \ name O or name CB )) or resid 592 through 602 or (resid 603 through 613 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 24 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 35 or (resid 36 through 39 and (na \ me N or name CA or name C or name O or name CB )) or resid 40 or (resid 41 and ( \ name N or name CA or name C or name O or name CB )) or resid 42 or (resid 43 thr \ ough 44 and (name N or name CA or name C or name O or name CB )) or resid 45 thr \ ough 50 or (resid 51 and (name N or name CA or name C or name O or name CB )) or \ resid 52 through 61 or (resid 62 and (name N or name CA or name C or name O or \ name CB )) or resid 63 through 66 or (resid 67 through 68 and (name N or name CA \ or name C or name O or name CB )) or resid 69 through 85 or (resid 86 and (name \ N or name CA or name C or name O or name CB )) or resid 87 through 92 or (resid \ 93 and (name N or name CA or name C or name O or name CB )) or resid 94 through \ 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) or r \ esid 111 through 129 or (resid 130 and (name N or name CA or name C or name O or \ name CB )) or resid 131 through 137 or (resid 138 and (name N or name CA or nam \ e C or name O or name CB )) or resid 139 or (resid 140 and (name N or name CA or \ name C or name O or name CB )) or resid 141 through 147 or (resid 148 and (name \ N or name CA or name C or name O or name CB )) or (resid 149 through 151 and (n \ ame N or name CA or name C or name O or name CB )) or resid 152 through 164 or ( \ resid 165 and (name N or name CA or name C or name O or name CB )) or resid 166 \ or (resid 167 through 169 and (name N or name CA or name C or name O or name CB \ )) or resid 170 through 180 or (resid 181 and (name N or name CA or name C or na \ me O or name CB )) or resid 182 or (resid 183 and (name N or name CA or name C o \ r name O or name CB )) or resid 184 through 189 or (resid 190 and (name N or nam \ e CA or name C or name O or name CB )) or resid 191 through 194 or (resid 195 th \ rough 197 and (name N or name CA or name C or name O or name CB )) or resid 198 \ or (resid 199 and (name N or name CA or name C or name O or name CB )) or resid \ 200 through 223 or (resid 224 through 225 and (name N or name CA or name C or na \ me O or name CB )) or resid 226 through 234 or (resid 235 and (name N or name CA \ or name C or name O or name CB )) or resid 236 through 250 or (resid 251 and (n \ ame N or name CA or name C or name O or name CB )) or resid 252 through 255 or ( \ resid 264 through 277 and (name N or name CA or name C or name O or name CB )) o \ r resid 278 through 289 or (resid 290 through 292 and (name N or name CA or name \ C or name O or name CB )) or resid 293 through 299 or (resid 300 through 305 an \ d (name N or name CA or name C or name O or name CB )) or resid 306 through 408 \ or (resid 409 and (name N or name CA or name C or name O or name CB )) or resid \ 410 or (resid 411 and (name N or name CA or name C or name O or name CB )) or re \ sid 412 through 415 or (resid 416 through 417 and (name N or name CA or name C o \ r name O or name CB )) or resid 424 through 440 or (resid 441 through 444 and (n \ ame N or name CA or name C or name O or name CB )) or resid 445 through 457 or ( \ resid 458 through 459 and (name N or name CA or name C or name O or name CB )) o \ r resid 460 through 461 or (resid 462 and (name N or name CA or name C or name O \ or name CB )) or resid 463 through 464 or (resid 465 and (name N or name CA or \ name C or name O or name CB )) or resid 466 through 489 or (resid 490 through 50 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 503 through \ 537 or (resid 538 and (name N or name CA or name C or name O or name CB )) or re \ sid 539 through 577 or (resid 578 through 580 and (name N or name CA or name C o \ r name O or name CB )) or resid 581 through 603 or (resid 604 through 613 and (n \ ame N or name CA or name C or name O or name CB )))) selection = (chain 'E' and ((resid 24 and (name N or name CA or name C or name O or name CB \ )) or resid 25 through 28 or (resid 29 and (name N or name CA or name C or name \ O or name CB )) or resid 30 or (resid 31 and (name N or name CA or name C or nam \ e O or name CB )) or resid 32 through 35 or (resid 36 through 39 and (name N or \ name CA or name C or name O or name CB )) or resid 40 through 42 or (resid 43 th \ rough 44 and (name N or name CA or name C or name O or name CB )) or resid 45 th \ rough 50 or (resid 51 and (name N or name CA or name C or name O or name CB )) o \ r resid 52 through 54 or (resid 55 and (name N or name CA or name C or name O or \ name CB )) or resid 56 through 61 or (resid 62 and (name N or name CA or name C \ or name O or name CB )) or resid 63 through 66 or (resid 67 through 68 and (nam \ e N or name CA or name C or name O or name CB )) or resid 69 through 70 or (resi \ d 71 and (name N or name CA or name C or name O or name CB )) or resid 72 throug \ h 79 or (resid 80 and (name N or name CA or name C or name O or name CB )) or re \ sid 81 through 82 or (resid 83 and (name N or name CA or name C or name O or nam \ e CB )) or resid 84 through 85 or (resid 86 and (name N or name CA or name C or \ name O or name CB )) or resid 87 through 92 or (resid 93 and (name N or name CA \ or name C or name O or name CB )) or resid 94 through 107 or (resid 108 and (nam \ e N or name CA or name C or name O or name CB )) or resid 109 through 133 or (re \ sid 134 and (name N or name CA or name C or name O or name CB )) or resid 135 th \ rough 150 or (resid 151 and (name N or name CA or name C or name O or name CB )) \ or resid 152 through 161 or (resid 162 and (name N or name CA or name C or name \ O or name CB )) or resid 163 or (resid 164 through 165 and (name N or name CA o \ r name C or name O or name CB )) or resid 166 or (resid 167 through 169 and (nam \ e N or name CA or name C or name O or name CB )) or resid 170 through 195 or (re \ sid 196 through 197 and (name N or name CA or name C or name O or name CB )) or \ resid 198 through 205 or (resid 206 through 208 and (name N or name CA or name C \ or name O or name CB )) or resid 209 or (resid 210 and (name N or name CA or na \ me C or name O or name CB )) or resid 211 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB )) or resid 219 through 250 or (resid \ 251 and (name N or name CA or name C or name O or name CB )) or resid 252 throug \ h 275 or (resid 276 through 277 and (name N or name CA or name C or name O or na \ me CB )) or resid 278 through 284 or (resid 285 and (name N or name CA or name C \ or name O or name CB )) or resid 286 through 288 or (resid 289 through 292 and \ (name N or name CA or name C or name O or name CB )) or resid 293 through 301 or \ (resid 302 through 305 and (name N or name CA or name C or name O or name CB )) \ or resid 306 through 310 or (resid 311 and (name N or name CA or name C or name \ O or name CB )) or resid 312 through 314 or (resid 315 and (name N or name CA o \ r name C or name O or name CB )) or resid 316 through 329 or (resid 330 through \ 332 and (name N or name CA or name C or name O or name CB )) or resid 333 throug \ h 361 or (resid 362 through 363 and (name N or name CA or name C or name O or na \ me CB )) or resid 364 through 365 or (resid 366 and (name N or name CA or name C \ or name O or name CB )) or resid 367 or (resid 368 and (name N or name CA or na \ me C or name O or name CB )) or resid 369 through 386 or (resid 387 and (name N \ or name CA or name C or name O or name CB )) or resid 388 through 406 or (resid \ 407 and (name N or name CA or name C or name O or name CB )) or resid 408 throug \ h 415 or (resid 416 through 425 and (name N or name CA or name C or name O or na \ me CB )) or resid 426 through 446 or (resid 447 through 449 and (name N or name \ CA or name C or name O or name CB )) or resid 450 or (resid 451 and (name N or n \ ame CA or name C or name O or name CB )) or resid 452 through 454 or (resid 455 \ through 459 and (name N or name CA or name C or name O or name CB )) or resid 46 \ 0 through 461 or (resid 462 and (name N or name CA or name C or name O or name C \ B )) or resid 463 through 479 or (resid 480 and (name N or name CA or name C or \ name O or name CB )) or resid 481 through 482 or (resid 483 and (name N or name \ CA or name C or name O or name CB )) or resid 484 through 490 or (resid 491 thro \ ugh 502 and (name N or name CA or name C or name O or name CB )) or (resid 503 t \ hrough 518 and (name N or name CA or name C or name O or name CB )) or resid 519 \ through 530 or (resid 531 through 536 and (name N or name CA or name C or name \ O or name CB )) or resid 537 through 551 or (resid 552 and (name N or name CA or \ name C or name O or name CB )) or resid 553 through 555 or (resid 556 through 5 \ 63 and (name N or name CA or name C or name O or name CB )) or (resid 564 throug \ h 574 and (name N or name CA or name C or name O or name CB )) or (resid 575 thr \ ough 580 and (name N or name CA or name C or name O or name CB )) or resid 581 o \ r (resid 582 through 584 and (name N or name CA or name C or name O or name CB ) \ ) or resid 585 through 586 or (resid 587 through 588 and (name N or name CA or n \ ame C or name O or name CB )) or resid 589 through 590 or (resid 591 and (name N \ or name CA or name C or name O or name CB )) or resid 592 through 602 or (resid \ 603 through 613 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'B' and (resid 15 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 80 or (resid 81 and (name N or nam \ e CA or name C or name O or name CB )) or resid 82 through 93 or (resid 94 and ( \ name N or name CA or name C or name O or name CB )) or resid 95 through 104 or ( \ resid 105 through 107 and (name N or name CA or name C or name O or name CB )) o \ r resid 108 through 115 or (resid 116 and (name N or name CA or name C or name O \ or name CB )) or resid 117 through 121 or (resid 122 and (name N or name CA or \ name C or name O or name CB )) or resid 123 through 128 or (resid 129 through 13 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 131 through \ 136 or (resid 137 and (name N or name CA or name C or name O or name CB )) or re \ sid 138 through 147 or (resid 148 through 149 and (name N or name CA or name C o \ r name O or name CB )) or resid 150 through 155 or (resid 156 through 157 and (n \ ame N or name CA or name C or name O or name CB )) or resid 158 through 159 or ( \ resid 160 and (name N or name CA or name C or name O or name CB )) or resid 161 \ through 173 or (resid 174 through 176 and (name N or name CA or name C or name O \ or name CB )) or resid 177 through 180 or (resid 181 through 182 and (name N or \ name CA or name C or name O or name CB )) or resid 183 through 193 or (resid 19 \ 4 and (name N or name CA or name C or name O or name CB )) or (resid 207 and (na \ me N or name CA or name C or name O or name CB )) or resid 208 through 217 or (r \ esid 218 and (name N or name CA or name C or name O or name CB )) or resid 219 t \ hrough 220 or (resid 221 through 223 and (name N or name CA or name C or name O \ or name CB )) or resid 224 through 225 or (resid 226 through 228 and (name N or \ name CA or name C or name O or name CB )) or resid 229 through 230 or (resid 231 \ through 232 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 33 or (resid 234 and (name N or name CA or name C or name O or name CB )) or res \ id 235 through 237 or (resid 238 through 239 and (name N or name CA or name C or \ name O or name CB )) or resid 240 through 245 or (resid 246 through 247 and (na \ me N or name CA or name C or name O or name CB )) or resid 248 through 250 or (r \ esid 251 and (name N or name CA or name C or name O or name CB )) or resid 252 t \ hrough 253 or (resid 254 and (name N or name CA or name C or name O or name CB ) \ ) or resid 255 through 270 or (resid 271 and (name N or name CA or name C or nam \ e O or name CB )) or resid 272 through 281 or (resid 282 through 283 and (name N \ or name CA or name C or name O or name CB )) or resid 284 through 296 or (resid \ 297 and (name N or name CA or name C or name O or name CB )) or resid 298 throu \ gh 300 or (resid 301 and (name N or name CA or name C or name O or name CB )) or \ resid 302 through 312 or (resid 313 and (name N or name CA or name C or name O \ or name CB )) or resid 314 through 316 or (resid 317 and (name N or name CA or n \ ame C or name O or name CB )) or resid 318 through 325 or (resid 326 and (name N \ or name CA or name C or name O or name CB )) or resid 327 through 356 or (resid \ 357 and (name N or name CA or name C or name O or name CB )) or resid 358 throu \ gh 375 or (resid 376 and (name N or name CA or name C or name O or name CB )) or \ resid 377 or (resid 378 and (name N or name CA or name C or name O or name CB ) \ ) or resid 379 or (resid 380 and (name N or name CA or name C or name O or name \ CB )) or resid 381 through 383 or (resid 384 through 387 and (name N or name CA \ or name C or name O or name CB )) or (resid 388 through 392 and (name N or name \ CA or name C or name O or name CB )) or resid 393 through 399 or (resid 400 thro \ ugh 401 and (name N or name CA or name C or name O or name CB )) or resid 402 th \ rough 416 or (resid 417 through 420 and (name N or name CA or name C or name O o \ r name CB )) or (resid 421 through 430 and (name N or name CA or name C or name \ O or name CB )) or resid 431 through 437 or (resid 438 and (name N or name CA or \ name C or name O or name CB )) or resid 439 or (resid 440 through 442 and (name \ N or name CA or name C or name O or name CB )) or resid 443 through 444 or (res \ id 445 and (name N or name CA or name C or name O or name CB )) or resid 446 thr \ ough 448 or (resid 449 and (name N or name CA or name C or name O or name CB )) \ or resid 450 or (resid 451 and (name N or name CA or name C or name O or name CB \ )) or resid 452 through 456 or (resid 457 and (name N or name CA or name C or n \ ame O or name CB )) or resid 458 or (resid 459 through 461 and (name N or name C \ A or name C or name O or name CB )) or resid 462 through 485)) selection = (chain 'D' and (resid 15 through 20 or (resid 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 through 31 or (resid 32 and (name N or nam \ e CA or name C or name O or name CB )) or resid 33 through 39 or (resid 40 and ( \ name N or name CA or name C or name O or name CB )) or resid 41 through 51 or (r \ esid 52 and (name N or name CA or name C or name O or name CB )) or resid 53 thr \ ough 55 or (resid 56 and (name N or name CA or name C or name O or name CB )) or \ resid 57 through 70 or (resid 71 and (name N or name CA or name C or name O or \ name CB )) or resid 72 through 132 or (resid 133 and (name N or name CA or name \ C or name O or name CB )) or resid 134 through 136 or (resid 137 and (name N or \ name CA or name C or name O or name CB )) or resid 138 through 155 or (resid 156 \ through 157 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 58 through 173 or (resid 174 through 176 and (name N or name CA or name C or nam \ e O or name CB )) or resid 177 through 193 or (resid 194 through 207 and (name N \ or name CA or name C or name O or name CB )) or resid 208 through 220 or (resid \ 221 through 223 and (name N or name CA or name C or name O or name CB )) or res \ id 224 through 231 or (resid 232 and (name N or name CA or name C or name O or n \ ame CB )) or resid 233 through 253 or (resid 254 and (name N or name CA or name \ C or name O or name CB )) or resid 255 through 263 or (resid 264 and (name N or \ name CA or name C or name O or name CB )) or resid 265 through 316 or (resid 317 \ and (name N or name CA or name C or name O or name CB )) or resid 318 through 3 \ 90 or (resid 391 through 392 and (name N or name CA or name C or name O or name \ CB )) or resid 393 or (resid 394 through 395 and (name N or name CA or name C or \ name O or name CB )) or resid 396 through 415 or (resid 416 through 420 and (na \ me N or name CA or name C or name O or name CB )) or (resid 421 through 430 and \ (name N or name CA or name C or name O or name CB )) or resid 431 or (resid 432 \ and (name N or name CA or name C or name O or name CB )) or resid 433 through 43 \ 9 or (resid 440 through 442 and (name N or name CA or name C or name O or name C \ B )) or resid 443 through 448 or (resid 449 and (name N or name CA or name C or \ name O or name CB )) or resid 450 through 455 or (resid 456 through 457 and (nam \ e N or name CA or name C or name O or name CB )) or resid 458 through 459 or (re \ sid 460 through 461 and (name N or name CA or name C or name O or name CB )) or \ resid 462 through 485)) selection = (chain 'F' and (resid 15 through 20 or (resid 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 or (resid 23 and (name N or name CA or nam \ e C or name O or name CB )) or resid 24 through 31 or (resid 32 and (name N or n \ ame CA or name C or name O or name CB )) or resid 33 through 34 or (resid 35 and \ (name N or name CA or name C or name O or name CB )) or resid 36 through 39 or \ (resid 40 and (name N or name CA or name C or name O or name CB )) or resid 41 t \ hrough 42 or (resid 43 and (name N or name CA or name C or name O or name CB )) \ or resid 44 through 50 or (resid 51 through 52 and (name N or name CA or name C \ or name O or name CB )) or resid 53 through 55 or (resid 56 and (name N or name \ CA or name C or name O or name CB )) or resid 57 through 60 or (resid 61 and (na \ me N or name CA or name C or name O or name CB )) or resid 62 through 83 or (res \ id 84 and (name N or name CA or name C or name O or name CB )) or resid 85 throu \ gh 93 or (resid 94 and (name N or name CA or name C or name O or name CB )) or r \ esid 95 through 128 or (resid 129 through 130 and (name N or name CA or name C o \ r name O or name CB )) or resid 131 through 180 or (resid 181 through 182 and (n \ ame N or name CA or name C or name O or name CB )) or resid 183 through 217 or ( \ resid 218 and (name N or name CA or name C or name O or name CB )) or resid 219 \ through 225 or (resid 226 through 228 and (name N or name CA or name C or name O \ or name CB )) or resid 229 through 237 or (resid 238 through 239 and (name N or \ name CA or name C or name O or name CB )) or resid 240 through 250 or (resid 25 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 252 through \ 263 or (resid 264 and (name N or name CA or name C or name O or name CB )) or re \ sid 265 through 281 or (resid 282 through 283 and (name N or name CA or name C o \ r name O or name CB )) or resid 284 through 312 or (resid 313 and (name N or nam \ e CA or name C or name O or name CB )) or resid 314 through 338 or (resid 339 th \ rough 341 and (name N or name CA or name C or name O or name CB )) or resid 342 \ through 347 or (resid 348 and (name N or name CA or name C or name O or name CB \ )) or resid 349 through 356 or (resid 357 and (name N or name CA or name C or na \ me O or name CB )) or resid 358 through 375 or (resid 376 and (name N or name CA \ or name C or name O or name CB )) or resid 377 through 391 or (resid 392 and (n \ ame N or name CA or name C or name O or name CB )) or resid 393 through 397 or ( \ resid 398 and (name N or name CA or name C or name O or name CB )) or resid 399 \ or (resid 400 through 401 and (name N or name CA or name C or name O or name CB \ )) or resid 402 through 444 or (resid 445 and (name N or name CA or name C or na \ me O or name CB )) or resid 446 through 455 or (resid 456 through 457 and (name \ N or name CA or name C or name O or name CB )) or resid 458 or (resid 459 throug \ h 461 and (name N or name CA or name C or name O or name CB )) or resid 462 or ( \ resid 463 and (name N or name CA or name C or name O or name CB )) or resid 464 \ through 473 or (resid 474 and (name N or name CA or name C or name O or name CB \ )) or resid 475 through 476 or (resid 477 and (name N or name CA or name C or na \ me O or name CB )) or resid 478 through 485)) } ncs_group { reference = (chain 'G' and ((resid 21 through 85 and (name N or name CA or name C or name O \ or name CB )) or resid 86 through 89 or (resid 90 through 91 and (name N or name \ CA or name C or name O or name CB )) or resid 92 through 94 or (resid 95 and (n \ ame N or name CA or name C or name O or name CB )) or resid 96 through 102 or (r \ esid 103 through 105 and (name N or name CA or name C or name O or name CB )) or \ resid 106 through 109 or (resid 110 through 116 and (name N or name CA or name \ C or name O or name CB )) or resid 117 through 122 or (resid 123 and (name N or \ name CA or name C or name O or name CB )) or resid 124 through 131 or (resid 132 \ and (name N or name CA or name C or name O or name CB )) or resid 133 through 1 \ 37 or (resid 138 and (name N or name CA or name C or name O or name CB )) or res \ id 139 or (resid 140 through 141 and (name N or name CA or name C or name O or n \ ame CB )) or resid 142 through 145 or (resid 146 through 148 and (name N or name \ CA or name C or name O or name CB )) or resid 149 through 162 or (resid 163 thr \ ough 167 and (name N or name CA or name C or name O or name CB )) or resid 168 t \ hrough 183 or (resid 184 through 185 and (name N or name CA or name C or name O \ or name CB )) or resid 186 through 193 or (resid 194 through 196 and (name N or \ name CA or name C or name O or name CB )) or resid 197 or (resid 198 and (name N \ or name CA or name C or name O or name CB )) or resid 199 through 231)) selection = (chain 'I' and (resid 21 through 89 or (resid 90 through 91 and (name N or name \ CA or name C or name O or name CB )) or resid 92 through 100 or (resid 101 throu \ gh 105 and (name N or name CA or name C or name O or name CB )) or resid 106 thr \ ough 121 or (resid 122 through 123 and (name N or name CA or name C or name O or \ name CB )) or resid 124 through 137 or (resid 138 and (name N or name CA or nam \ e C or name O or name CB )) or resid 139 or (resid 140 through 141 and (name N o \ r name CA or name C or name O or name CB )) or resid 142 through 143 or (resid 1 \ 44 through 148 and (name N or name CA or name C or name O or name CB )) or resid \ 149 through 191 or (resid 192 through 196 and (name N or name CA or name C or n \ ame O or name CB )) or resid 197 or (resid 198 and (name N or name CA or name C \ or name O or name CB )) or resid 199 through 219 or (resid 220 through 221 and ( \ name N or name CA or name C or name O or name CB )) or resid 222 through 227 or \ (resid 228 and (name N or name CA or name C or name O or name CB )) or resid 229 \ through 231)) selection = (chain 'K' and ((resid 21 through 85 and (name N or name CA or name C or name O \ or name CB )) or resid 86 through 94 or (resid 95 and (name N or name CA or name \ C or name O or name CB )) or resid 96 through 131 or (resid 132 and (name N or \ name CA or name C or name O or name CB )) or resid 133 through 135 or (resid 136 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 39 through 143 or (resid 144 through 148 and (name N or name CA or name C or nam \ e O or name CB )) or resid 149 through 152 or (resid 153 through 155 and (name N \ or name CA or name C or name O or name CB )) or resid 156 through 158 or (resid \ 159 and (name N or name CA or name C or name O or name CB )) or resid 160 throu \ gh 162 or (resid 163 through 167 and (name N or name CA or name C or name O or n \ ame CB )) or resid 168 through 219 or (resid 220 through 221 and (name N or name \ CA or name C or name O or name CB )) or resid 222 through 230 or (resid 231 and \ (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'H' and ((resid 14 through 77 and (name N or name CA or name C or name O \ or name CB )) or resid 78 or (resid 79 through 93 and (name N or name CA or name \ C or name O or name CB )) or resid 94 through 102 or (resid 103 through 104 and \ (name N or name CA or name C or name O or name CB )) or resid 105 through 112)) \ selection = (chain 'J' and ((resid 14 through 93 and (name N or name CA or name C or name O \ or name CB )) or resid 94 or (resid 95 through 97 and (name N or name CA or name \ C or name O or name CB )) or resid 98 or (resid 99 through 100 and (name N or n \ ame CA or name C or name O or name CB )) or resid 101 through 102 or (resid 103 \ through 104 and (name N or name CA or name C or name O or name CB )) or resid 10 \ 5 through 108 or (resid 109 and (name N or name CA or name C or name O or name C \ B )) or resid 110 or (resid 111 through 112 and (name N or name CA or name C or \ name O or name CB )))) selection = (chain 'L' and ((resid 14 through 93 and (name N or name CA or name C or name O \ or name CB )) or resid 94 or (resid 95 through 97 and (name N or name CA or name \ C or name O or name CB )) or resid 98 or (resid 99 through 100 and (name N or n \ ame CA or name C or name O or name CB )) or resid 101 through 108 or (resid 109 \ and (name N or name CA or name C or name O or name CB )) or resid 110 through 11 \ 2)) } 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 group one per residue 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: 2.580 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: 1.300 Check model and map are aligned: 0.240 Set scattering table: 0.300 Process input model: 87.220 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 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 : 0.005 0.053 34274 Z= 0.196 Angle : 0.539 10.487 47130 Z= 0.279 Chirality : 0.042 0.169 5918 Planarity : 0.004 0.056 6176 Dihedral : 11.398 110.640 10462 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.04 % Allowed : 0.36 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.12), residues: 5188 helix: 2.50 (0.10), residues: 2624 sheet: -1.94 (0.21), residues: 550 loop : -0.09 (0.15), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 541 HIS 0.004 0.001 HIS A 213 PHE 0.022 0.001 PHE A 451 TYR 0.019 0.001 TYR C 272 ARG 0.008 0.000 ARG E 344 Details of bonding type rmsd hydrogen bonds : bond 0.15088 ( 2387) hydrogen bonds : angle 6.47345 ( 7026) covalent geometry : bond 0.00471 (34274) covalent geometry : angle 0.53948 (47130) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 363 time to evaluate : 4.054 Fit side-chains REVERT: B 369 ILE cc_start: 0.9167 (mt) cc_final: 0.8906 (mt) REVERT: B 438 LYS cc_start: 0.8596 (mtmm) cc_final: 0.8342 (mtmm) REVERT: D 366 ASN cc_start: 0.9019 (m-40) cc_final: 0.8736 (m110) REVERT: D 374 ASN cc_start: 0.8595 (p0) cc_final: 0.8377 (p0) REVERT: M 42 ARG cc_start: 0.7801 (tpp80) cc_final: 0.7194 (ttp80) outliers start: 1 outliers final: 0 residues processed: 363 average time/residue: 0.4312 time to fit residues: 259.6313 Evaluate side-chains 306 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 3.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 435 optimal weight: 0.0470 chunk 391 optimal weight: 5.9990 chunk 217 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 263 optimal weight: 0.1980 chunk 208 optimal weight: 2.9990 chunk 404 optimal weight: 0.5980 chunk 156 optimal weight: 5.9990 chunk 245 optimal weight: 0.9990 chunk 301 optimal weight: 0.3980 chunk 468 optimal weight: 10.0000 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.135058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.101357 restraints weight = 50144.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.099806 restraints weight = 30429.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.101718 restraints weight = 21048.353| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34274 Z= 0.120 Angle : 0.490 10.622 47130 Z= 0.255 Chirality : 0.041 0.177 5918 Planarity : 0.004 0.045 6176 Dihedral : 4.252 105.294 5536 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.98 % Allowed : 7.77 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.12), residues: 5188 helix: 2.66 (0.10), residues: 2634 sheet: -1.90 (0.21), residues: 547 loop : -0.02 (0.15), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 541 HIS 0.005 0.001 HIS B 273 PHE 0.021 0.001 PHE A 451 TYR 0.013 0.001 TYR E 463 ARG 0.006 0.000 ARG B 166 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 2387) hydrogen bonds : angle 4.64458 ( 7026) covalent geometry : bond 0.00264 (34274) covalent geometry : angle 0.48971 (47130) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 355 time to evaluate : 3.946 Fit side-chains REVERT: B 76 ILE cc_start: 0.8650 (mm) cc_final: 0.8318 (mt) REVERT: B 369 ILE cc_start: 0.9084 (mt) cc_final: 0.8833 (mt) REVERT: C 199 GLU cc_start: 0.8446 (tt0) cc_final: 0.8183 (tt0) REVERT: F 337 MET cc_start: 0.8457 (ptt) cc_final: 0.8198 (ptp) REVERT: K 136 LYS cc_start: 0.8358 (mtpp) cc_final: 0.8149 (mtpp) REVERT: L 83 ILE cc_start: 0.8561 (tt) cc_final: 0.8169 (mt) REVERT: M 61 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8781 (mmm) outliers start: 22 outliers final: 10 residues processed: 362 average time/residue: 0.4892 time to fit residues: 296.6664 Evaluate side-chains 326 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 315 time to evaluate : 3.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 570 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain M residue 61 MET Chi-restraints excluded: chain M residue 178 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 180 optimal weight: 0.9980 chunk 300 optimal weight: 0.0670 chunk 38 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 473 optimal weight: 10.0000 chunk 285 optimal weight: 1.9990 chunk 477 optimal weight: 6.9990 chunk 367 optimal weight: 6.9990 chunk 251 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 356 optimal weight: 4.9990 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 HIS ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN C 323 ASN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.130760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.096935 restraints weight = 51079.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.094907 restraints weight = 31731.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.096373 restraints weight = 22457.604| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 34274 Z= 0.266 Angle : 0.574 10.352 47130 Z= 0.295 Chirality : 0.044 0.192 5918 Planarity : 0.004 0.049 6176 Dihedral : 4.387 98.986 5536 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.58 % Allowed : 11.50 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.12), residues: 5188 helix: 2.59 (0.10), residues: 2639 sheet: -2.12 (0.20), residues: 587 loop : -0.07 (0.15), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 541 HIS 0.007 0.001 HIS A 213 PHE 0.025 0.002 PHE A 451 TYR 0.015 0.001 TYR E 463 ARG 0.009 0.000 ARG E 344 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 2387) hydrogen bonds : angle 4.62312 ( 7026) covalent geometry : bond 0.00642 (34274) covalent geometry : angle 0.57388 (47130) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 319 time to evaluate : 3.642 Fit side-chains REVERT: B 76 ILE cc_start: 0.8832 (mm) cc_final: 0.8568 (mt) REVERT: B 369 ILE cc_start: 0.9187 (mt) cc_final: 0.8926 (mt) REVERT: B 438 LYS cc_start: 0.8698 (mtmm) cc_final: 0.8459 (mtmm) REVERT: C 45 MET cc_start: 0.8646 (mtt) cc_final: 0.8242 (mtt) REVERT: C 199 GLU cc_start: 0.8494 (tt0) cc_final: 0.8171 (tt0) REVERT: M 42 ARG cc_start: 0.7969 (tpp80) cc_final: 0.7423 (tpp80) outliers start: 58 outliers final: 42 residues processed: 358 average time/residue: 0.4372 time to fit residues: 259.7326 Evaluate side-chains 346 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 304 time to evaluate : 3.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 570 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain M residue 60 VAL Chi-restraints excluded: chain M residue 61 MET Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 170 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain O residue 306 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 331 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 394 optimal weight: 1.9990 chunk 357 optimal weight: 0.6980 chunk 210 optimal weight: 0.8980 chunk 80 optimal weight: 0.0870 chunk 312 optimal weight: 50.0000 chunk 69 optimal weight: 0.6980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 207 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.100196 restraints weight = 50269.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.099335 restraints weight = 28514.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.100498 restraints weight = 19790.456| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34274 Z= 0.125 Angle : 0.473 8.937 47130 Z= 0.244 Chirality : 0.041 0.174 5918 Planarity : 0.003 0.047 6176 Dihedral : 4.149 95.902 5536 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.13 % Allowed : 13.77 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.12), residues: 5188 helix: 2.75 (0.10), residues: 2622 sheet: -2.05 (0.20), residues: 580 loop : 0.03 (0.15), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 541 HIS 0.005 0.001 HIS B 273 PHE 0.016 0.001 PHE A 451 TYR 0.013 0.001 TYR E 534 ARG 0.005 0.000 ARG F 302 Details of bonding type rmsd hydrogen bonds : bond 0.03106 ( 2387) hydrogen bonds : angle 4.32816 ( 7026) covalent geometry : bond 0.00289 (34274) covalent geometry : angle 0.47291 (47130) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 340 time to evaluate : 4.208 Fit side-chains REVERT: B 76 ILE cc_start: 0.8702 (mm) cc_final: 0.8437 (mt) REVERT: B 150 MET cc_start: 0.8275 (ttp) cc_final: 0.8072 (ttp) REVERT: B 369 ILE cc_start: 0.9101 (mt) cc_final: 0.8836 (mt) REVERT: C 61 ILE cc_start: 0.9244 (mm) cc_final: 0.8795 (mt) REVERT: D 215 MET cc_start: 0.8998 (mtm) cc_final: 0.8785 (ptp) REVERT: D 399 VAL cc_start: 0.8921 (t) cc_final: 0.8716 (t) REVERT: F 34 VAL cc_start: 0.8405 (OUTLIER) cc_final: 0.8152 (m) REVERT: M 42 ARG cc_start: 0.7897 (tpp80) cc_final: 0.7075 (ttp80) REVERT: M 61 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8761 (mmm) outliers start: 48 outliers final: 28 residues processed: 370 average time/residue: 0.4353 time to fit residues: 269.2407 Evaluate side-chains 344 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 314 time to evaluate : 3.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 570 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain K residue 190 VAL Chi-restraints excluded: chain M residue 61 MET Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain O residue 306 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 279 optimal weight: 0.8980 chunk 319 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 346 optimal weight: 30.0000 chunk 123 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 377 optimal weight: 30.0000 chunk 113 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN C 323 ASN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.133196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.099590 restraints weight = 50390.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.098103 restraints weight = 29260.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.099323 restraints weight = 20862.003| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 34274 Z= 0.167 Angle : 0.491 9.490 47130 Z= 0.252 Chirality : 0.042 0.183 5918 Planarity : 0.004 0.047 6176 Dihedral : 4.103 83.233 5536 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.75 % Allowed : 14.21 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.12), residues: 5188 helix: 2.77 (0.10), residues: 2620 sheet: -2.01 (0.21), residues: 564 loop : 0.01 (0.15), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 541 HIS 0.005 0.001 HIS A 213 PHE 0.015 0.001 PHE A 451 TYR 0.016 0.001 TYR O 296 ARG 0.006 0.000 ARG F 302 Details of bonding type rmsd hydrogen bonds : bond 0.03142 ( 2387) hydrogen bonds : angle 4.27627 ( 7026) covalent geometry : bond 0.00399 (34274) covalent geometry : angle 0.49055 (47130) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 324 time to evaluate : 3.996 Fit side-chains REVERT: B 76 ILE cc_start: 0.8805 (mm) cc_final: 0.8494 (mt) REVERT: B 150 MET cc_start: 0.8316 (ttp) cc_final: 0.8035 (ttp) REVERT: B 369 ILE cc_start: 0.9122 (mt) cc_final: 0.8853 (mt) REVERT: C 61 ILE cc_start: 0.9159 (mm) cc_final: 0.8856 (mt) REVERT: C 199 GLU cc_start: 0.8479 (tt0) cc_final: 0.8181 (tt0) REVERT: D 399 VAL cc_start: 0.8909 (t) cc_final: 0.8709 (t) REVERT: M 42 ARG cc_start: 0.8003 (tpp80) cc_final: 0.7661 (tpp80) REVERT: N 5 ARG cc_start: 0.8221 (tpt-90) cc_final: 0.7881 (tpt-90) outliers start: 62 outliers final: 45 residues processed: 366 average time/residue: 0.4436 time to fit residues: 272.2924 Evaluate side-chains 361 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 316 time to evaluate : 3.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 570 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain K residue 190 VAL Chi-restraints excluded: chain M residue 61 MET Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain O residue 306 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 215 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 318 optimal weight: 0.5980 chunk 475 optimal weight: 50.0000 chunk 76 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 484 optimal weight: 50.0000 chunk 78 optimal weight: 0.6980 chunk 390 optimal weight: 4.9990 chunk 385 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.133943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.100460 restraints weight = 50175.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.098905 restraints weight = 29470.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.100052 restraints weight = 21769.817| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 34274 Z= 0.147 Angle : 0.479 9.544 47130 Z= 0.245 Chirality : 0.041 0.179 5918 Planarity : 0.003 0.047 6176 Dihedral : 4.000 69.519 5536 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.53 % Allowed : 15.10 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.12), residues: 5188 helix: 2.80 (0.10), residues: 2625 sheet: -1.91 (0.20), residues: 601 loop : 0.03 (0.15), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 541 HIS 0.004 0.001 HIS A 213 PHE 0.015 0.001 PHE A 451 TYR 0.013 0.001 TYR E 534 ARG 0.006 0.000 ARG K 144 Details of bonding type rmsd hydrogen bonds : bond 0.03039 ( 2387) hydrogen bonds : angle 4.19826 ( 7026) covalent geometry : bond 0.00348 (34274) covalent geometry : angle 0.47882 (47130) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 331 time to evaluate : 3.986 Fit side-chains REVERT: B 76 ILE cc_start: 0.8783 (mm) cc_final: 0.8509 (mt) REVERT: B 150 MET cc_start: 0.8287 (ttp) cc_final: 0.7754 (ttt) REVERT: B 369 ILE cc_start: 0.9109 (mt) cc_final: 0.8836 (mt) REVERT: C 45 MET cc_start: 0.8706 (mmm) cc_final: 0.8460 (mmm) REVERT: C 61 ILE cc_start: 0.9183 (mm) cc_final: 0.8728 (mt) REVERT: C 199 GLU cc_start: 0.8463 (tt0) cc_final: 0.8176 (tt0) REVERT: D 399 VAL cc_start: 0.8896 (t) cc_final: 0.8692 (t) REVERT: E 40 MET cc_start: 0.8660 (tpt) cc_final: 0.8080 (tpt) REVERT: E 515 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8633 (tt) REVERT: F 34 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.8153 (m) REVERT: F 161 MET cc_start: 0.8627 (mtp) cc_final: 0.8382 (mtp) REVERT: I 101 GLU cc_start: 0.8284 (tp30) cc_final: 0.8073 (tp30) REVERT: M 42 ARG cc_start: 0.8049 (tpp80) cc_final: 0.7193 (ttp80) REVERT: M 61 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8781 (mmm) outliers start: 57 outliers final: 46 residues processed: 370 average time/residue: 0.4449 time to fit residues: 277.3211 Evaluate side-chains 365 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 316 time to evaluate : 4.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 24 TYR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 570 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain I residue 172 ILE Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain K residue 190 VAL Chi-restraints excluded: chain M residue 61 MET Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain O residue 306 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 333 optimal weight: 50.0000 chunk 87 optimal weight: 0.9990 chunk 336 optimal weight: 50.0000 chunk 402 optimal weight: 6.9990 chunk 423 optimal weight: 3.9990 chunk 474 optimal weight: 10.0000 chunk 260 optimal weight: 0.6980 chunk 156 optimal weight: 0.7980 chunk 473 optimal weight: 30.0000 chunk 448 optimal weight: 40.0000 chunk 319 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN B 243 ASN ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN C 323 ASN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.132174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.100035 restraints weight = 50737.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.099219 restraints weight = 31293.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.099711 restraints weight = 21603.467| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 34274 Z= 0.220 Angle : 0.528 10.032 47130 Z= 0.269 Chirality : 0.043 0.186 5918 Planarity : 0.004 0.048 6176 Dihedral : 4.074 61.500 5536 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.93 % Allowed : 15.41 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.12), residues: 5188 helix: 2.75 (0.10), residues: 2627 sheet: -2.05 (0.21), residues: 576 loop : -0.02 (0.15), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 541 HIS 0.006 0.001 HIS A 213 PHE 0.017 0.001 PHE C 297 TYR 0.017 0.001 TYR C 272 ARG 0.008 0.000 ARG E 344 Details of bonding type rmsd hydrogen bonds : bond 0.03197 ( 2387) hydrogen bonds : angle 4.28049 ( 7026) covalent geometry : bond 0.00532 (34274) covalent geometry : angle 0.52818 (47130) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 312 time to evaluate : 3.900 Fit side-chains REVERT: B 76 ILE cc_start: 0.8843 (mm) cc_final: 0.8579 (mt) REVERT: B 150 MET cc_start: 0.8284 (ttp) cc_final: 0.7787 (ttt) REVERT: B 369 ILE cc_start: 0.9119 (mt) cc_final: 0.8830 (mt) REVERT: C 45 MET cc_start: 0.8699 (mmm) cc_final: 0.8448 (mmm) REVERT: C 61 ILE cc_start: 0.9207 (mm) cc_final: 0.8762 (mt) REVERT: C 199 GLU cc_start: 0.8405 (tt0) cc_final: 0.8117 (tt0) REVERT: D 399 VAL cc_start: 0.8940 (t) cc_final: 0.8734 (t) REVERT: E 515 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8699 (tt) REVERT: F 227 GLN cc_start: 0.7884 (tt0) cc_final: 0.7679 (tt0) REVERT: M 33 LYS cc_start: 0.8261 (ttpt) cc_final: 0.8013 (ttmt) REVERT: M 42 ARG cc_start: 0.8184 (tpp80) cc_final: 0.7540 (tpp80) outliers start: 66 outliers final: 57 residues processed: 358 average time/residue: 0.4342 time to fit residues: 261.9781 Evaluate side-chains 365 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 307 time to evaluate : 3.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 24 TYR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 570 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain I residue 172 ILE Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain K residue 190 VAL Chi-restraints excluded: chain M residue 61 MET Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain O residue 306 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 249 optimal weight: 2.9990 chunk 187 optimal weight: 0.5980 chunk 481 optimal weight: 50.0000 chunk 20 optimal weight: 0.6980 chunk 337 optimal weight: 20.0000 chunk 416 optimal weight: 40.0000 chunk 38 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 390 optimal weight: 0.7980 chunk 334 optimal weight: 50.0000 chunk 514 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.133180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.099673 restraints weight = 50030.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.097812 restraints weight = 30507.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.098898 restraints weight = 22154.480| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 34274 Z= 0.160 Angle : 0.493 9.623 47130 Z= 0.252 Chirality : 0.042 0.185 5918 Planarity : 0.003 0.047 6176 Dihedral : 3.998 52.770 5536 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.80 % Allowed : 15.81 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.12), residues: 5188 helix: 2.78 (0.10), residues: 2627 sheet: -2.03 (0.21), residues: 574 loop : 0.01 (0.15), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 541 HIS 0.004 0.001 HIS A 213 PHE 0.014 0.001 PHE A 451 TYR 0.013 0.001 TYR C 272 ARG 0.007 0.000 ARG K 144 Details of bonding type rmsd hydrogen bonds : bond 0.03076 ( 2387) hydrogen bonds : angle 4.21789 ( 7026) covalent geometry : bond 0.00383 (34274) covalent geometry : angle 0.49303 (47130) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 323 time to evaluate : 3.707 Fit side-chains REVERT: B 76 ILE cc_start: 0.8802 (mm) cc_final: 0.8538 (mt) REVERT: B 150 MET cc_start: 0.8266 (ttp) cc_final: 0.7791 (ttt) REVERT: B 369 ILE cc_start: 0.9116 (mt) cc_final: 0.8849 (mt) REVERT: C 45 MET cc_start: 0.8706 (mmm) cc_final: 0.8480 (mmm) REVERT: C 61 ILE cc_start: 0.9206 (mm) cc_final: 0.8769 (mt) REVERT: C 199 GLU cc_start: 0.8473 (tt0) cc_final: 0.8186 (tt0) REVERT: D 399 VAL cc_start: 0.8909 (t) cc_final: 0.8691 (t) REVERT: E 40 MET cc_start: 0.8644 (tpt) cc_final: 0.8109 (tpt) REVERT: M 42 ARG cc_start: 0.8151 (tpp80) cc_final: 0.7506 (tpp80) REVERT: M 61 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8777 (mmm) outliers start: 63 outliers final: 57 residues processed: 367 average time/residue: 0.4774 time to fit residues: 291.9249 Evaluate side-chains 375 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 317 time to evaluate : 6.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 24 TYR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 570 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain I residue 172 ILE Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain K residue 190 VAL Chi-restraints excluded: chain M residue 61 MET Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain O residue 306 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 17 optimal weight: 0.6980 chunk 215 optimal weight: 0.3980 chunk 63 optimal weight: 0.9990 chunk 327 optimal weight: 5.9990 chunk 368 optimal weight: 10.0000 chunk 278 optimal weight: 0.5980 chunk 227 optimal weight: 0.0970 chunk 159 optimal weight: 20.0000 chunk 416 optimal weight: 40.0000 chunk 348 optimal weight: 10.0000 chunk 306 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 207 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.135035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.101379 restraints weight = 49935.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.100365 restraints weight = 27873.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.101598 restraints weight = 19680.044| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34274 Z= 0.116 Angle : 0.464 9.210 47130 Z= 0.237 Chirality : 0.041 0.180 5918 Planarity : 0.003 0.046 6176 Dihedral : 3.821 40.116 5536 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.53 % Allowed : 16.47 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.13), residues: 5188 helix: 2.86 (0.10), residues: 2625 sheet: -1.91 (0.20), residues: 632 loop : 0.09 (0.15), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 541 HIS 0.003 0.001 HIS A 170 PHE 0.012 0.001 PHE A 451 TYR 0.019 0.001 TYR C 272 ARG 0.007 0.000 ARG K 144 Details of bonding type rmsd hydrogen bonds : bond 0.02896 ( 2387) hydrogen bonds : angle 4.07633 ( 7026) covalent geometry : bond 0.00272 (34274) covalent geometry : angle 0.46377 (47130) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 342 time to evaluate : 5.400 Fit side-chains REVERT: B 76 ILE cc_start: 0.8716 (mm) cc_final: 0.8406 (mt) REVERT: B 150 MET cc_start: 0.8253 (ttp) cc_final: 0.7893 (ttt) REVERT: B 369 ILE cc_start: 0.9060 (mt) cc_final: 0.8793 (mt) REVERT: C 199 GLU cc_start: 0.8489 (tt0) cc_final: 0.8206 (tt0) REVERT: E 40 MET cc_start: 0.8606 (tpt) cc_final: 0.8159 (tpt) REVERT: E 515 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8595 (tt) REVERT: F 34 VAL cc_start: 0.8405 (OUTLIER) cc_final: 0.8144 (m) REVERT: M 42 ARG cc_start: 0.8056 (tpp80) cc_final: 0.7422 (tpp80) REVERT: M 61 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8736 (mmm) REVERT: M 189 ASN cc_start: 0.8469 (t0) cc_final: 0.8238 (m-40) outliers start: 57 outliers final: 48 residues processed: 383 average time/residue: 0.5294 time to fit residues: 345.7578 Evaluate side-chains 373 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 322 time to evaluate : 4.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 570 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain G residue 223 TYR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain I residue 172 ILE Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain K residue 190 VAL Chi-restraints excluded: chain M residue 61 MET Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain O residue 306 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 462 optimal weight: 30.0000 chunk 502 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 323 optimal weight: 1.9990 chunk 500 optimal weight: 30.0000 chunk 335 optimal weight: 50.0000 chunk 336 optimal weight: 40.0000 chunk 68 optimal weight: 0.4980 chunk 208 optimal weight: 0.2980 chunk 515 optimal weight: 5.9990 chunk 383 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 GLN C 320 ASN C 323 ASN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.131598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.099553 restraints weight = 50566.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.098927 restraints weight = 31308.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.098998 restraints weight = 22045.763| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 34274 Z= 0.250 Angle : 0.554 10.842 47130 Z= 0.283 Chirality : 0.044 0.247 5918 Planarity : 0.004 0.048 6176 Dihedral : 4.065 37.686 5536 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.75 % Allowed : 16.30 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.12), residues: 5188 helix: 2.75 (0.10), residues: 2627 sheet: -2.16 (0.20), residues: 595 loop : -0.02 (0.15), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 541 HIS 0.007 0.001 HIS A 213 PHE 0.019 0.001 PHE A 451 TYR 0.021 0.001 TYR C 272 ARG 0.010 0.001 ARG E 344 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 2387) hydrogen bonds : angle 4.28200 ( 7026) covalent geometry : bond 0.00603 (34274) covalent geometry : angle 0.55422 (47130) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 308 time to evaluate : 3.976 Fit side-chains REVERT: B 76 ILE cc_start: 0.8872 (mm) cc_final: 0.8554 (mt) REVERT: B 150 MET cc_start: 0.8285 (ttp) cc_final: 0.7853 (ttt) REVERT: B 369 ILE cc_start: 0.9147 (mt) cc_final: 0.8856 (mt) REVERT: C 61 ILE cc_start: 0.9154 (mm) cc_final: 0.8719 (mt) REVERT: C 199 GLU cc_start: 0.8467 (tt0) cc_final: 0.8178 (tt0) REVERT: E 515 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8742 (tt) REVERT: M 42 ARG cc_start: 0.8180 (tpp80) cc_final: 0.7564 (tpp80) outliers start: 62 outliers final: 53 residues processed: 352 average time/residue: 0.4627 time to fit residues: 275.5685 Evaluate side-chains 358 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 304 time to evaluate : 4.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 320 ASN Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain E residue 24 TYR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 570 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain I residue 172 ILE Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain K residue 190 VAL Chi-restraints excluded: chain M residue 61 MET Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain O residue 306 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 243 optimal weight: 0.0870 chunk 216 optimal weight: 0.7980 chunk 8 optimal weight: 0.4980 chunk 509 optimal weight: 30.0000 chunk 234 optimal weight: 0.9980 chunk 491 optimal weight: 30.0000 chunk 454 optimal weight: 30.0000 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 268 optimal weight: 0.4980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.134752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.100678 restraints weight = 49994.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.099807 restraints weight = 27415.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.100968 restraints weight = 19648.951| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34274 Z= 0.115 Angle : 0.472 9.913 47130 Z= 0.242 Chirality : 0.041 0.236 5918 Planarity : 0.003 0.047 6176 Dihedral : 3.890 39.470 5536 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.26 % Allowed : 17.10 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.13), residues: 5188 helix: 2.85 (0.10), residues: 2620 sheet: -1.98 (0.20), residues: 630 loop : 0.07 (0.15), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 541 HIS 0.003 0.001 HIS A 170 PHE 0.015 0.001 PHE A 451 TYR 0.023 0.001 TYR C 272 ARG 0.008 0.000 ARG K 144 Details of bonding type rmsd hydrogen bonds : bond 0.02931 ( 2387) hydrogen bonds : angle 4.12511 ( 7026) covalent geometry : bond 0.00261 (34274) covalent geometry : angle 0.47214 (47130) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10849.73 seconds wall clock time: 193 minutes 53.62 seconds (11633.62 seconds total)