Starting phenix.real_space_refine on Fri Jun 27 10:02:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tmo_25997/06_2025/7tmo_25997.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tmo_25997/06_2025/7tmo_25997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tmo_25997/06_2025/7tmo_25997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tmo_25997/06_2025/7tmo_25997.map" model { file = "/net/cci-nas-00/data/ceres_data/7tmo_25997/06_2025/7tmo_25997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tmo_25997/06_2025/7tmo_25997.cif" } resolution = 3.3 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= 0.126 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 20130 2.51 5 N 5698 2.21 5 O 5642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31559 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 4285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4285 Classifications: {'peptide': 592} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 561} Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 353 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 23, 'GLU:plan': 25, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 198 Chain: "B" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3390 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 22, 'ASN:plan1': 5, 'ARG:plan': 3, 'ASP:plan': 21} Unresolved non-hydrogen planarities: 189 Chain: "C" Number of atoms: 3690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 3690 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 261} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 554} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 860 Unresolved non-hydrogen angles: 1073 Unresolved non-hydrogen dihedrals: 704 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 12, 'ARG:plan': 11, 'TYR:plan': 5, 'ASN:plan1': 12, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 10, 'GLU:plan': 38, 'ASP:plan': 31} Unresolved non-hydrogen planarities: 513 Chain: "D" Number of atoms: 3306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3306 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 433} Chain breaks: 1 Unresolved non-hydrogen bonds: 295 Unresolved non-hydrogen angles: 362 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 24, 'ASN:plan1': 10, 'ARG:plan': 3, 'ASP:plan': 22} Unresolved non-hydrogen planarities: 215 Chain: "E" Number of atoms: 4113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4113 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 559} Unresolved non-hydrogen bonds: 445 Unresolved non-hydrogen angles: 542 Unresolved non-hydrogen dihedrals: 352 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 7, 'ASP:plan': 27, 'PHE:plan': 2, 'GLU:plan': 35, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 298 Chain: "F" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3317 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 433} Chain breaks: 1 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 30, 'ARG:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 16} Unresolved non-hydrogen planarities: 211 Chain: "G" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1273 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 5, 'TRANS': 194} Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 390 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 11, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 20, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 198 Chain: "H" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 456 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 90 Chain: "I" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1326 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 5, 'TRANS': 211} Unresolved non-hydrogen bonds: 416 Unresolved non-hydrogen angles: 509 Unresolved non-hydrogen dihedrals: 335 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 11, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 25, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 249 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: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1308 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 5, 'TRANS': 200} Unresolved non-hydrogen bonds: 339 Unresolved non-hydrogen angles: 416 Unresolved non-hydrogen dihedrals: 267 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 10, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 26, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 213 Chain: "L" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 486 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 1, 'TRANS': 86} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 260 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 118 Chain: "M" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1235 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 3, 'TRANS': 210} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 504 Unresolved non-hydrogen angles: 631 Unresolved non-hydrogen dihedrals: 403 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 13, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 5, 'GLU:plan': 19, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 300 Chain: "N" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 551 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 105} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 354 Unresolved non-hydrogen angles: 454 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 9, 'PHE:plan': 6, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 196 Chain: "P" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 2193 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 410} Link IDs: {'PTRANS': 9, 'TRANS': 431} Chain breaks: 2 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1426 Unresolved non-hydrogen angles: 1821 Unresolved non-hydrogen dihedrals: 1158 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.25, per 1000 atoms: 0.58 Number of scatterers: 31559 At special positions: 0 Unit cell: (142.14, 165.83, 185.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 82 16.00 P 5 15.00 Mg 2 11.99 O 5642 8.00 N 5698 7.00 C 20130 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: 7.77 Conformation dependent library (CDL) restraints added in 4.5 seconds 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8998 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 43 sheets defined 54.6% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.02 Creating SS restraints... Processing helix chain 'A' and resid 111 through 120 Processing helix chain 'A' and resid 237 through 243 Processing helix chain 'A' and resid 261 through 273 Processing helix chain 'A' and resid 286 through 297 removed outlier: 3.690A pdb=" N MET A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.878A pdb=" N GLY A 306 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 346 removed outlier: 4.130A pdb=" N ALA A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 372 Processing helix chain 'A' and resid 383 through 394 Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 442 through 447 Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 477 through 503 removed outlier: 3.885A pdb=" N LEU A 501 " --> pdb=" O GLN A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 525 Processing helix chain 'A' and resid 539 through 564 Processing helix chain 'A' and resid 566 through 574 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 615 removed outlier: 3.712A pdb=" N SER A 614 " --> pdb=" O ARG A 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 155 through 161 Processing helix chain 'B' and resid 179 through 191 Processing helix chain 'B' and resid 218 through 232 Processing helix chain 'B' and resid 233 through 238 removed outlier: 3.658A pdb=" N GLU B 236 " --> pdb=" O GLY B 233 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR B 238 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 269 removed outlier: 4.141A pdb=" N ARG B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 295 Processing helix chain 'B' and resid 307 through 317 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 Processing helix chain 'B' and resid 426 through 443 Processing helix chain 'B' and resid 453 through 468 removed outlier: 4.125A pdb=" N TYR B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) 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 265 through 272 Processing helix chain 'C' and resid 286 through 300 Proline residue: C 298 - end of helix Processing helix chain 'C' and resid 310 through 313 Processing helix chain 'C' and resid 325 through 345 removed outlier: 4.894A pdb=" N ILE C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N TYR C 334 " --> pdb=" O GLU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 372 Processing helix chain 'C' and resid 383 through 395 removed outlier: 3.959A pdb=" N ALA C 395 " --> pdb=" O PHE C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 422 removed outlier: 3.675A pdb=" N GLY C 421 " --> pdb=" O PRO C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 435 Processing helix chain 'C' and resid 442 through 448 Processing helix chain 'C' and resid 463 through 475 removed outlier: 4.522A pdb=" N LYS C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE C 470 " --> pdb=" O VAL C 466 " (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 532 through 536 removed outlier: 3.793A pdb=" N ALA C 536 " --> pdb=" O THR C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 564 Processing helix chain 'C' and resid 566 through 574 Processing helix chain 'C' and resid 574 through 587 removed outlier: 3.727A pdb=" N LYS C 585 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE C 586 " --> pdb=" O SER C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 615 removed outlier: 3.694A pdb=" N HIS C 597 " --> pdb=" O GLU C 593 " (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 162 Processing helix chain 'D' and resid 179 through 191 Processing helix chain 'D' and resid 218 through 232 Processing helix chain 'D' and resid 233 through 238 removed outlier: 3.579A pdb=" N GLU D 236 " --> pdb=" O GLY D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 271 Proline residue: D 256 - end of helix Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 307 through 318 Processing helix chain 'D' and resid 337 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 removed outlier: 3.586A pdb=" N ALA D 386 " --> pdb=" O LEU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 421 removed outlier: 4.192A pdb=" N ALA D 418 " --> pdb=" O ALA D 414 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL D 419 " --> pdb=" O ALA D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 442 removed outlier: 3.578A pdb=" N SER D 432 " --> pdb=" O GLU D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 466 Processing helix chain 'D' and resid 477 through 485 Processing helix chain 'E' and resid 111 through 120 Processing helix chain 'E' and resid 237 through 244 Processing helix chain 'E' and resid 261 through 272 Processing helix chain 'E' and resid 286 through 297 removed outlier: 3.587A pdb=" N MET E 290 " --> pdb=" O ARG E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 346 removed outlier: 3.931A pdb=" N ILE E 333 " --> pdb=" O ARG E 329 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 372 Processing helix chain 'E' and resid 383 through 393 Processing helix chain 'E' and resid 418 through 422 removed outlier: 3.954A pdb=" N ASP E 422 " --> pdb=" O ALA E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 435 Processing helix chain 'E' and resid 442 through 448 Processing helix chain 'E' and resid 463 through 474 removed outlier: 4.825A pdb=" N LYS E 469 " --> pdb=" O ASN E 465 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE E 470 " --> pdb=" O VAL E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 503 Processing helix chain 'E' and resid 508 through 525 Processing helix chain 'E' and resid 539 through 564 Processing helix chain 'E' and resid 566 through 574 Processing helix chain 'E' and resid 574 through 584 Processing helix chain 'E' and resid 588 through 590 No H-bonds generated for 'chain 'E' and resid 588 through 590' Processing helix chain 'E' and resid 591 through 613 removed outlier: 4.282A pdb=" N GLU E 595 " --> pdb=" O ARG E 591 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA E 612 " --> pdb=" O GLN E 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 109 removed outlier: 3.910A 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 233 Processing helix chain 'F' and resid 234 through 236 No H-bonds generated for 'chain 'F' and resid 234 through 236' Processing helix chain 'F' and resid 250 through 270 removed outlier: 3.902A pdb=" N ILE F 254 " --> pdb=" O ILE F 250 " (cutoff:3.500A) Proline residue: F 256 - end of helix Processing helix chain 'F' and resid 280 through 295 Processing helix chain 'F' and resid 300 through 304 Processing helix chain 'F' and resid 307 through 317 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 420 Processing helix chain 'F' and resid 421 through 425 Processing helix chain 'F' and resid 426 through 442 Processing helix chain 'F' and resid 453 through 466 Processing helix chain 'F' and resid 477 through 485 Processing helix chain 'G' and resid 33 through 114 removed outlier: 3.568A pdb=" N ILE G 80 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG G 114 " --> pdb=" O ILE G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 133 removed outlier: 3.513A pdb=" N LYS G 131 " --> pdb=" O GLU G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 164 removed outlier: 4.618A pdb=" N ASP G 147 " --> pdb=" O GLU G 143 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU G 148 " --> pdb=" O ARG G 144 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ASP G 154 " --> pdb=" O GLU G 150 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASP G 155 " --> pdb=" O SER G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 214 Processing helix chain 'G' and resid 214 through 224 Processing helix chain 'H' and resid 33 through 61 removed outlier: 4.140A pdb=" N ASN H 61 " --> pdb=" O PHE H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 103 removed outlier: 3.589A pdb=" N GLU H 67 " --> pdb=" O GLY H 63 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ASP H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ASP H 93 " --> pdb=" O LYS H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 114 removed outlier: 3.699A pdb=" N GLU I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA I 111 " --> pdb=" O LEU I 107 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG I 114 " --> pdb=" O ILE I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 131 removed outlier: 3.560A pdb=" N LEU I 121 " --> pdb=" O TYR I 117 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL I 126 " --> pdb=" O GLN I 122 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS I 131 " --> pdb=" O GLU I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 152 Processing helix chain 'I' and resid 152 through 164 Processing helix chain 'I' and resid 202 through 223 removed outlier: 3.677A pdb=" N GLU I 212 " --> pdb=" O LYS I 208 " (cutoff:3.500A) Proline residue: I 216 - end of helix Processing helix chain 'J' and resid 6 through 63 removed outlier: 3.912A pdb=" N ALA J 35 " --> pdb=" O LYS J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 104 removed outlier: 3.667A pdb=" N GLY J 78 " --> pdb=" O ALA J 74 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU J 79 " --> pdb=" O GLY J 75 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ASP J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASP J 93 " --> pdb=" O LYS J 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 113 removed outlier: 3.909A pdb=" N ARG K 52 " --> pdb=" O THR K 48 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN K 53 " --> pdb=" O ASN K 49 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN K 57 " --> pdb=" O ASN K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 133 Proline residue: K 119 - end of helix removed outlier: 3.873A pdb=" N ALA K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS K 131 " --> pdb=" O GLU K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 164 removed outlier: 5.395A pdb=" N ASP K 154 " --> pdb=" O GLU K 150 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASP K 155 " --> pdb=" O SER K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 214 Processing helix chain 'K' and resid 214 through 224 Processing helix chain 'L' and resid 26 through 68 removed outlier: 3.592A pdb=" N LYS L 33 " --> pdb=" O GLN L 29 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA L 40 " --> pdb=" O LYS L 36 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY L 64 " --> pdb=" O LYS L 60 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY L 66 " --> pdb=" O ALA L 62 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU L 68 " --> pdb=" O GLY L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 104 removed outlier: 3.858A pdb=" N GLY L 78 " --> pdb=" O ALA L 74 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU L 79 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ASP L 92 " --> pdb=" O GLU L 88 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASP L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 11 through 76 Processing helix chain 'M' and resid 79 through 86 Processing helix chain 'M' and resid 128 through 217 Proline residue: M 179 - end of helix 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: 3.730A pdb=" N ASN N 76 " --> pdb=" O HIS N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 84 Processing helix chain 'N' and resid 106 through 111 removed outlier: 3.609A pdb=" N ARG N 111 " --> pdb=" O SER N 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 23 removed outlier: 3.743A pdb=" N ARG P 23 " --> pdb=" O ILE P 19 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 33 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 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 Processing helix chain 'P' and resid 135 through 152 removed outlier: 4.128A pdb=" N GLN P 152 " --> pdb=" O SER P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 167 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 210 Processing helix chain 'P' and resid 210 through 223 removed outlier: 3.804A pdb=" N LEU P 214 " --> pdb=" O PHE P 210 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 256 removed outlier: 4.223A pdb=" N ASN P 256 " --> pdb=" O LEU P 252 " (cutoff:3.500A) Processing helix chain 'P' and resid 256 through 267 removed outlier: 3.617A pdb=" N GLN P 265 " --> pdb=" O ASN P 261 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR P 267 " --> pdb=" O LEU P 263 " (cutoff:3.500A) Processing helix chain 'P' and resid 269 through 281 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 Processing helix chain 'P' and resid 332 through 353 removed outlier: 3.745A 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 removed outlier: 3.539A pdb=" N VAL P 375 " --> pdb=" O SER P 371 " (cutoff:3.500A) Processing helix chain 'P' and resid 376 through 408 removed outlier: 5.042A pdb=" N ASP P 385 " --> pdb=" O SER P 381 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLU P 386 " --> pdb=" O ASP P 382 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASP P 390 " --> pdb=" O GLU P 386 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN P 391 " --> pdb=" O PHE P 387 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ILE P 394 " --> pdb=" O ASP P 390 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N PHE P 395 " --> pdb=" O ASN P 391 " (cutoff:3.500A) Processing helix chain 'P' and resid 409 through 411 No H-bonds generated for 'chain 'P' and resid 409 through 411' Processing helix chain 'P' and resid 413 through 433 Processing helix chain 'P' and resid 435 through 444 removed outlier: 4.106A pdb=" N ASP P 439 " --> pdb=" O PRO P 435 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL P 440 " --> pdb=" O GLU P 436 " (cutoff:3.500A) Processing helix chain 'P' and resid 445 through 455 removed outlier: 3.781A pdb=" N ASN P 455 " --> pdb=" O MET P 451 " (cutoff:3.500A) Processing helix chain 'P' and resid 458 through 473 Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.077A pdb=" N ARG B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE B 70 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE B 76 " --> pdb=" O LEU B 68 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 25 through 31 current: chain 'B' and resid 92 through 99 removed outlier: 4.323A pdb=" N LEU B 26 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILE G 197 " --> pdb=" O ASN G 192 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA G 137 " --> pdb=" O VAL G 173 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.077A pdb=" N ARG B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE B 70 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE B 76 " --> pdb=" O LEU B 68 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 62 through 71 current: chain 'A' and resid 47 through 51 removed outlier: 4.562A pdb=" N GLU A 47 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A 69 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL A 30 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE A 36 " --> pdb=" O TYR A 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 25 through 31 current: chain 'B' and resid 92 through 99 removed outlier: 4.323A pdb=" N LEU B 26 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILE G 197 " --> pdb=" O ASN G 192 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA G 137 " --> pdb=" O VAL G 173 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 96 Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105 removed outlier: 6.365A pdb=" N ILE A 278 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL A 318 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N TYR A 280 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ASN A 320 " --> pdb=" O TYR A 280 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLY A 282 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 277 " --> pdb=" O ASN A 349 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 279 " --> pdb=" O SER A 351 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU A 225 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 173 removed outlier: 3.872A 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: 6.799A pdb=" N GLU A 199 " --> pdb=" O THR A 183 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 413 through 414 removed outlier: 6.195A pdb=" N THR A 252 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 301 through 302 removed outlier: 3.575A pdb=" N GLU A 309 " --> pdb=" O THR A 302 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 101 through 104 Processing sheet with id=AB1, first strand: chain 'B' and resid 112 through 113 removed outlier: 3.584A pdb=" N MET B 215 " --> pdb=" O THR B 279 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLY B 327 " --> pdb=" O VAL B 322 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL B 322 " --> pdb=" O GLY B 327 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE B 329 " --> pdb=" O GLY B 320 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG B 321 " --> pdb=" O ILE B 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 150 through 151 removed outlier: 4.485A pdb=" N ILE B 164 " --> pdb=" O ILE B 151 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 173 removed outlier: 6.568A pdb=" N PHE B 173 " --> pdb=" O VAL B 360 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N GLN B 357 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N LEU B 376 " --> pdb=" O GLN B 357 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE B 359 " --> pdb=" O ASN B 374 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 26 through 30 removed outlier: 6.419A pdb=" N ILE C 36 " --> pdb=" O TYR C 28 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS C 67 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG C 62 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN C 71 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL C 60 " --> pdb=" O GLN C 71 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU C 47 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEU C 48 " --> pdb=" O THR C 88 " (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: 6.921A pdb=" N ILE C 278 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL C 318 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TYR C 280 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA C 277 " --> pdb=" O SER C 351 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ILE C 353 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE C 279 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL C 350 " --> pdb=" O SER C 411 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL C 413 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N MET C 352 " --> pdb=" O VAL C 413 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ALA C 415 " --> pdb=" O MET C 352 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ALA C 354 " --> pdb=" O ALA C 415 " (cutoff:3.500A) removed outlier: 3.878A 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: 6.921A pdb=" N ILE C 278 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL C 318 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TYR C 280 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA C 277 " --> pdb=" O SER C 351 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ILE C 353 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE C 279 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL C 350 " --> pdb=" O SER C 411 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL C 413 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N MET C 352 " --> pdb=" O VAL C 413 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ALA C 415 " --> pdb=" O MET C 352 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ALA C 354 " --> pdb=" O ALA C 415 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR C 252 " --> pdb=" O ALA C 414 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 437 " --> pdb=" O THR C 251 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 170 through 173 removed outlier: 4.043A pdb=" N GLY C 159 " --> pdb=" O ILE C 172 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 151 through 152 removed outlier: 6.560A pdb=" N GLU C 199 " --> pdb=" O THR C 183 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 232 through 233 removed outlier: 4.642A pdb=" N CYS C 246 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 375 through 377 removed outlier: 6.232A pdb=" N PHE C 380 " --> pdb=" O ALA C 376 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 56 through 57 removed outlier: 7.417A pdb=" N LEU E 48 " --> pdb=" O THR E 88 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU E 86 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ILE E 27 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLU E 38 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR E 69 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA D 75 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ARG D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE D 70 " --> pdb=" O ARG D 74 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE D 76 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN D 66 " --> pdb=" O GLN D 78 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLU D 51 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE D 52 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU D 26 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL I 173 " --> pdb=" O ALA I 137 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 101 through 104 Processing sheet with id=AC5, first strand: chain 'D' and resid 112 through 113 removed outlier: 6.564A pdb=" N PHE D 212 " --> pdb=" O PHE D 241 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ASN D 243 " --> pdb=" O PHE D 212 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ALA D 214 " --> pdb=" O ASN D 243 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA D 213 " --> pdb=" O THR D 279 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 144 through 145 removed outlier: 4.317A pdb=" N ARG D 321 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 151 through 152 Processing sheet with id=AC8, first strand: chain 'D' and resid 172 through 173 removed outlier: 5.602A pdb=" N PHE D 359 " --> pdb=" O PRO D 377 " (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: 6.723A pdb=" N ILE E 279 " --> pdb=" O ILE E 353 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU E 225 " --> pdb=" O VAL E 399 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 104 through 105 removed outlier: 6.723A pdb=" N ILE E 279 " --> pdb=" O ILE E 353 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR E 251 " --> pdb=" O VAL E 437 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 139 through 141 Processing sheet with id=AD4, first strand: chain 'E' and resid 151 through 152 removed outlier: 6.522A pdb=" N GLU E 199 " --> pdb=" O THR E 183 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 157 through 161 removed outlier: 4.174A pdb=" N GLY E 159 " --> pdb=" O ILE E 172 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 232 through 233 removed outlier: 4.536A pdb=" N CYS E 246 " --> pdb=" O LEU E 233 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 301 through 302 Processing sheet with id=AD8, first strand: chain 'F' and resid 38 through 41 removed outlier: 3.580A pdb=" N LEU F 41 " --> pdb=" O ALA F 75 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA F 75 " --> pdb=" O LEU F 41 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE F 76 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU F 26 " --> pdb=" O PHE F 95 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 101 through 104 removed outlier: 3.525A pdb=" N LEU F 132 " --> pdb=" O ILE F 102 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 112 through 113 removed outlier: 6.766A pdb=" N SER F 209 " --> pdb=" O LEU F 275 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE F 277 " --> pdb=" O SER F 209 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL F 211 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N THR F 279 " --> pdb=" O VAL F 211 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA F 213 " --> pdb=" O THR F 279 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.296A pdb=" N ARG F 321 " --> pdb=" O ILE F 145 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 164 through 165 removed outlier: 4.450A pdb=" N ILE F 164 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY F 192 " --> pdb=" O SER F 152 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 334 through 336 Processing sheet with id=AE5, first strand: chain 'M' and resid 92 through 98 Processing sheet with id=AE6, first strand: chain 'N' and resid 8 through 10 removed outlier: 6.409A pdb=" N ALA N 9 " --> pdb=" O LEU N 68 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ASN N 70 " --> pdb=" O ALA N 9 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 28 through 29 2212 hydrogen bonds defined for protein. 6423 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: 14.13 Time building geometry restraints manager: 9.24 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: 10697 1.34 - 1.46: 4000 1.46 - 1.57: 17214 1.57 - 1.69: 8 1.69 - 1.81: 148 Bond restraints: 32067 Sorted by residual: bond pdb=" CA THR E 88 " pdb=" CB THR E 88 " ideal model delta sigma weight residual 1.528 1.553 -0.025 1.56e-02 4.11e+03 2.56e+00 bond pdb=" CA THR E 88 " pdb=" C THR E 88 " ideal model delta sigma weight residual 1.523 1.541 -0.018 1.30e-02 5.92e+03 1.88e+00 bond pdb=" C LEU D 376 " pdb=" N PRO D 377 " ideal model delta sigma weight residual 1.336 1.348 -0.012 9.80e-03 1.04e+04 1.58e+00 bond pdb=" N THR E 88 " pdb=" CA THR E 88 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.21e-02 6.83e+03 1.29e+00 bond pdb=" CG1 ILE F 315 " pdb=" CD1 ILE F 315 " ideal model delta sigma weight residual 1.513 1.469 0.044 3.90e-02 6.57e+02 1.26e+00 ... (remaining 32062 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 43526 2.00 - 4.00: 426 4.00 - 6.00: 48 6.00 - 8.00: 1 8.00 - 10.00: 3 Bond angle restraints: 44004 Sorted by residual: angle pdb=" N ILE B 120 " pdb=" CA ILE B 120 " pdb=" C ILE B 120 " ideal model delta sigma weight residual 111.91 107.46 4.45 8.90e-01 1.26e+00 2.50e+01 angle pdb=" N MET F 161 " pdb=" CA MET F 161 " pdb=" CB MET F 161 " ideal model delta sigma weight residual 114.17 109.79 4.38 1.14e+00 7.69e-01 1.48e+01 angle pdb=" C LYS D 367 " pdb=" N GLY D 368 " pdb=" CA GLY D 368 " ideal model delta sigma weight residual 122.16 119.44 2.72 7.70e-01 1.69e+00 1.25e+01 angle pdb=" N THR E 88 " pdb=" CA THR E 88 " pdb=" C THR E 88 " ideal model delta sigma weight residual 111.28 114.86 -3.58 1.09e+00 8.42e-01 1.08e+01 angle pdb=" N GLY D 368 " pdb=" CA GLY D 368 " pdb=" C GLY D 368 " ideal model delta sigma weight residual 111.16 116.56 -5.40 1.76e+00 3.23e-01 9.40e+00 ... (remaining 43999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.54: 18526 28.54 - 57.09: 455 57.09 - 85.63: 26 85.63 - 114.17: 8 114.17 - 142.71: 2 Dihedral angle restraints: 19017 sinusoidal: 5087 harmonic: 13930 Sorted by residual: dihedral pdb=" C5' ADP E 701 " pdb=" O5' ADP E 701 " pdb=" PA ADP E 701 " pdb=" O2A ADP E 701 " ideal model delta sinusoidal sigma weight residual 300.00 157.29 142.71 1 2.00e+01 2.50e-03 4.31e+01 dihedral pdb=" O2A ADP E 701 " pdb=" O3A ADP E 701 " pdb=" PA ADP E 701 " pdb=" PB ADP E 701 " ideal model delta sinusoidal sigma weight residual -60.00 62.17 -122.17 1 2.00e+01 2.50e-03 3.68e+01 dihedral pdb=" O1B ADP E 701 " pdb=" O3A ADP E 701 " pdb=" PB ADP E 701 " pdb=" PA ADP E 701 " ideal model delta sinusoidal sigma weight residual -60.00 38.00 -98.00 1 2.00e+01 2.50e-03 2.73e+01 ... (remaining 19014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4241 0.045 - 0.090: 959 0.090 - 0.136: 273 0.136 - 0.181: 11 0.181 - 0.226: 5 Chirality restraints: 5489 Sorted by residual: chirality pdb=" CB ILE E 108 " pdb=" CA ILE E 108 " pdb=" CG1 ILE E 108 " pdb=" CG2 ILE E 108 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CG LEU D 258 " pdb=" CB LEU D 258 " pdb=" CD1 LEU D 258 " pdb=" CD2 LEU D 258 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB ILE C 167 " pdb=" CA ILE C 167 " pdb=" CG1 ILE C 167 " pdb=" CG2 ILE C 167 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 5486 not shown) Planarity restraints: 5734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE M 178 " 0.045 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO M 179 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO M 179 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO M 179 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU M 174 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.73e+00 pdb=" C GLU M 174 " 0.041 2.00e-02 2.50e+03 pdb=" O GLU M 174 " -0.016 2.00e-02 2.50e+03 pdb=" N HIS M 175 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 477 " 0.039 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO B 478 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 478 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 478 " 0.033 5.00e-02 4.00e+02 ... (remaining 5731 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 105 2.53 - 3.12: 24630 3.12 - 3.72: 51939 3.72 - 4.31: 66039 4.31 - 4.90: 115740 Nonbonded interactions: 258453 Sorted by model distance: nonbonded pdb=" OG1 THR A 263 " pdb="MG MG A 702 " model vdw 1.942 2.170 nonbonded pdb=" O1G ATP A 701 " pdb="MG MG A 702 " model vdw 1.988 2.170 nonbonded pdb=" OG1 THR E 263 " pdb="MG MG E 702 " model vdw 2.053 2.170 nonbonded pdb=" NH1 ARG G 206 " pdb=" O VAL H 102 " model vdw 2.199 3.120 nonbonded pdb=" O LYS B 438 " pdb=" OG1 THR B 442 " model vdw 2.211 3.040 ... (remaining 258448 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 37 or (resid 38 through 39 and (name N or name \ CA or name C or name O or name CB )) or resid 40 through 49 or (resid 50 through \ 51 and (name N or name CA or name C or name O or name CB )) or resid 52 through \ 53 or (resid 54 through 55 and (name N or name CA or name C or name O or name C \ B )) or resid 56 through 65 or (resid 66 and (name N or name CA or name C or nam \ e O or name CB )) or resid 67 through 85 or (resid 86 and (name N or name CA or \ name C or name O or name CB )) or resid 87 through 89 or (resid 90 and (name N o \ r name CA or name C or name O or name CB )) or resid 91 through 100 or (resid 10 \ 1 through 102 and (name N or name CA or name C or name O or name CB )) or resid \ 103 through 112 or (resid 113 through 114 and (name N or name CA or name C or na \ me O or name CB )) or resid 115 through 118 or (resid 119 and (name N or name CA \ or name C or name O or name CB )) or resid 120 through 129 or (resid 130 and (n \ ame 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 (resid 138 and (name N or name CA or name 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 re \ sid 141 through 147 or (resid 148 and (name N or name CA or name C or name O or \ name CB )) or resid 149 or (resid 150 through 151 and (name N or name CA or name \ C or name O or name CB )) or resid 152 through 159 or (resid 160 and (name N or \ name CA or name C or name O or name CB )) or resid 161 through 163 or (resid 16 \ 4 through 166 and (name N or name CA or name C or name O or name CB )) or resid \ 167 or (resid 168 through 169 and (name N or name CA or name C or name O or name \ CB )) or resid 170 through 178 or (resid 179 and (name N or name CA or name C o \ r name O or name CB )) or resid 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 name O or name CB )) or resid 191 or (resid 192 and (n \ ame N or name CA or name C or name O or name CB )) or resid 193 or (resid 194 th \ rough 196 and (name N or name CA or name C or name O or name CB )) or resid 197 \ through 198 or (resid 199 and (name N or name CA or name C or name O or name CB \ )) or resid 200 or (resid 201 through 203 and (name N or name CA or name C or na \ me O or name CB )) or (resid 204 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 name \ C or name O or name CB )) or resid 211 through 223 or (resid 224 through 226 and \ (name N or name CA or name C or name O or name CB )) or resid 227 through 234 o \ r (resid 235 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 36 or (resid 237 through 238 and (name N or name CA or name C or name O or name \ CB )) or resid 239 through 242 or (resid 243 and (name N or name CA or name C or \ name O or name CB )) or resid 244 through 256 or (resid 264 through 268 and (na \ me N or name CA or name C or name O or name CB )) or resid 269 or (resid 270 thr \ ough 271 and (name N or name CA or name C or name O or name CB )) or resid 272 o \ r (resid 273 through 277 and (name N or name CA or name C or name O or name CB ) \ ) or resid 278 through 282 or (resid 283 and (name N or name CA or name C or nam \ e O or name CB )) or (resid 284 through 286 and (name N or name CA or name C or \ name O or name CB )) or resid 287 or (resid 288 through 305 and (name N or name \ CA or name C or name O or name CB )) or (resid 306 through 311 and (name N or na \ me CA or name C or name O or name CB )) or resid 312 or (resid 313 and (name N o \ r name CA or name C or name O or name CB )) or resid 314 or (resid 315 and (name \ N or name CA or name C or name O or name CB )) or resid 316 through 319 or (res \ id 320 and (name N or name CA or name C or name O or name CB )) or resid 321 thr \ ough 329 or (resid 330 through 331 and (name N or name CA or name C or name O or \ name CB )) or resid 332 through 350 or (resid 351 and (name N or name CA or nam \ e C or name O or name CB )) or resid 352 through 354 or (resid 355 through 357 a \ nd (name N or name CA or name C or name O or name CB )) or resid 358 or (resid 3 \ 59 and (name N or name CA or name C or name O or name CB )) or resid 360 through \ 361 or (resid 362 through 363 and (name N or name CA or name C or name O or nam \ e 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 372 or (resid 373 and (name N or na \ me CA or name C or name O or name CB )) or resid 374 through 377 or (resid 378 a \ nd (name N or name CA or name C or name O or name CB )) or resid 379 through 389 \ or (resid 390 and (name N or name CA or name C or name O or name CB )) or resid \ 391 through 392 or (resid 393 and (name N or name CA or name C or name O or nam \ e CB )) or resid 394 through 404 or (resid 405 and (name N or name CA or name C \ or name O or name CB )) or resid 406 or (resid 407 and (name N or name CA or nam \ e C or name O or name CB )) or resid 408 or (resid 409 and (name N or name CA or \ name C or name O or name CB )) or resid 410 through 416 or (resid 417 through 4 \ 19 and (name N or name CA or name C or name O or name CB )) or (resid 420 throug \ h 425 and (name N or name CA or name C or name O or name CB )) or resid 426 or ( \ resid 427 through 430 and (name N or name CA or name C or name O or name CB )) o \ r resid 431 through 440 or (resid 441 through 451 and (name N or name CA or name \ C or name O or name CB )) or resid 452 or (resid 453 through 459 and (name N or \ name CA or name C or name O or name CB )) or resid 460 or (resid 461 through 46 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 463 or (resi \ d 464 through 465 and (name N or name CA or name C or name O or name CB )) or re \ sid 466 through 473 or (resid 474 and (name N or name CA or name C or name O or \ name CB )) or resid 475 through 479 or (resid 480 and (name N or name CA or name \ C or name O or name CB )) or resid 481 or (resid 482 through 484 and (name N or \ name CA or name C or name O or name CB )) or resid 485 or (resid 486 through 48 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 488 or (resi \ d 489 through 502 and (name N or name CA or name C or name O or name CB )) or re \ sid 503 or (resid 504 through 521 and (name N or name CA or name C or name O or \ name CB )) or resid 522 through 526 or (resid 527 through 529 and (name N or nam \ e CA or name C or name O or name CB )) or resid 530 or (resid 531 through 539 an \ d (name N or name CA or name C or name O or name CB )) or resid 540 through 541 \ or (resid 542 and (name N or name CA or name C or name O or name CB )) or resid \ 543 through 544 or (resid 545 through 563 and (name N or name CA or name C or na \ me O or name CB )) or (resid 564 through 574 and (name N or name CA or name C or \ name O or name CB )) or (resid 575 through 591 and (name N or name CA or name C \ or name O or name CB )) or (resid 592 through 597 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 598 through 613 and (name N or name CA or \ name C or name O or name CB )))) selection = (chain 'C' and (resid 24 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 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 49 or (resid 50 through 51 and (name N or name CA or name C or name O or na \ me CB )) or resid 52 through 92 or (resid 93 and (name N or name CA or name C or \ name O or name CB )) or resid 94 through 129 or (resid 130 and (name N or name \ CA or name C or name O or name CB )) or resid 131 through 180 or (resid 181 and \ (name N or name CA or name C or name O or name CB )) or resid 182 through 223 or \ (resid 224 through 226 and (name N or name CA or name C or name O or name CB )) \ or resid 227 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 (name N or name CA o \ r name C or name O or name CB )) or resid 252 through 267 or (resid 268 and (nam \ e N or name CA or name C or name O or name CB )) or resid 269 through 273 or (re \ sid 274 through 277 and (name N or name CA or name C or name O or name CB )) or \ resid 278 through 356 or (resid 357 and (name N or name CA or name C or name O o \ r name CB )) or resid 358 through 415 or (resid 416 through 419 and (name N or n \ ame CA or name C or name O or name CB )) or resid 420 through 613)) 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 through 35 or (resid 36 through 39 and (name N or na \ me CA or name C or name O or name CB )) or resid 40 through 42 or (resid 43 thro \ ugh 44 and (name N or name CA or name C or name O or name CB )) or resid 45 thro \ ugh 50 or (resid 51 and (name N or name CA or name C or name O or name CB )) or \ resid 52 through 54 or (resid 55 and (name N or name CA or name C or name O or n \ ame CB )) or resid 56 through 85 or (resid 86 and (name N or name CA or name C o \ r name O or name CB )) or resid 87 through 92 or (resid 93 and (name N or name C \ A or name C or name O or name CB )) or resid 94 through 100 or (resid 101 throug \ h 102 and (name N or name CA or name C or name O or name CB )) or resid 103 thro \ ugh 112 or (resid 113 through 114 and (name N or name CA or name C or name O or \ name CB )) or resid 115 through 133 or (resid 134 and (name N or name CA or name \ C or name O or name CB )) or resid 135 through 139 or (resid 140 and (name N or \ name CA or name C or name O or name CB )) or resid 141 through 150 or (resid 15 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 152 through \ 163 or (resid 164 through 166 and (name N or name CA or name C or name O or name \ CB )) or resid 167 through 191 or (resid 192 and (name N or name CA or name C o \ r name O or name CB )) or resid 193 through 195 or (resid 196 and (name N or nam \ e CA or name C or name O or name CB )) or resid 197 through 205 or (resid 206 th \ rough 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 \ 211 through 225 or (resid 226 and (name N or name CA or name C or name O or name \ CB )) or resid 227 through 236 or (resid 237 through 238 and (name N or name CA \ or name C or name O or name CB )) or resid 239 through 242 or (resid 243 and (n \ ame N or name CA or name C or name O or name CB )) or resid 244 through 250 or ( \ resid 251 and (name N or name CA or name C or name O or name CB )) or resid 252 \ through 256 or (resid 264 through 268 and (name N or name CA or name C or name O \ or name CB )) or resid 269 through 270 or (resid 271 and (name N or name CA or \ name C or name O or name CB )) or resid 272 through 282 or (resid 283 and (name \ N or name CA or name C or name O or name CB )) or (resid 284 through 286 and (na \ me N or name CA or name C or name O or name CB )) or resid 287 or (resid 288 thr \ ough 305 and (name N or name CA or name C or name O or name CB )) or (resid 306 \ through 311 and (name N or name CA or name C or name O or name CB )) or resid 31 \ 2 or (resid 313 and (name N or name CA or name C or name O or name CB )) or resi \ d 314 or (resid 315 and (name N or name CA or name C or name O or name CB )) or \ resid 316 through 319 or (resid 320 and (name N or name CA or name C or name O o \ r name CB )) or resid 321 through 329 or (resid 330 through 331 and (name N or n \ ame CA or name C or name O or name CB )) or resid 332 through 350 or (resid 351 \ and (name N or name CA or name C or name O or name CB )) or resid 352 through 35 \ 8 or (resid 359 and (name N or name CA or name C or name O or name CB )) or resi \ d 360 through 404 or (resid 405 and (name N or name CA or name C or name O or na \ me CB )) or resid 406 or (resid 407 and (name N or name CA or name C or name O o \ r name CB )) or resid 408 through 415 or (resid 416 through 419 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 420 through 425 and (name N o \ r name CA or name C or name O or name CB )) or resid 426 or (resid 427 through 4 \ 30 and (name N or name CA or name C or name O or name CB )) or resid 431 through \ 440 or (resid 441 through 451 and (name N or name CA or name C or name O or nam \ e CB )) or resid 452 through 453 or (resid 454 through 459 and (name N or name C \ A or name C or name O or name CB )) or 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 or (resid 464 t \ hrough 465 and (name N or name CA or name C or name O or name CB )) or resid 466 \ through 479 or (resid 480 and (name N or name CA or name C or name O or name CB \ )) or resid 481 or (resid 482 through 484 and (name N or name CA or name C or n \ ame O or name CB )) or resid 485 or (resid 486 through 487 and (name N or name C \ A or name C or name O or name CB )) or resid 488 or (resid 489 through 502 and ( \ name N or name CA or name C or name O or name CB )) or (resid 503 through 521 an \ d (name N or name CA or name C or name O or name CB )) or resid 522 through 527 \ or (resid 528 through 529 and (name N or name CA or name C or name O or name CB \ )) or resid 530 or (resid 531 through 539 and (name N or name CA or name C or na \ me O or name CB )) or resid 540 through 541 or (resid 542 and (name N or name CA \ or name C or name O or name CB )) or resid 543 through 544 or (resid 545 throug \ h 563 and (name N or name CA or name C or name O or name CB )) or (resid 564 thr \ ough 574 and (name N or name CA or name C or name O or name CB )) or (resid 575 \ through 591 and (name N or name CA or name C or name O or name CB )) or resid 59 \ 2 or (resid 593 through 597 and (name N or name CA or name C or name O or name C \ B )) or (resid 598 through 613 and (name N or name CA or name C or name O or nam \ e CB )))) } ncs_group { reference = (chain 'B' and ((resid 15 through 18 and (name N or name CA or name C or name O \ or name CB )) or resid 19 through 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 (n \ ame N or name CA or name C or name O or name CB )) or resid 53 through 60 or (re \ sid 61 and (name N or name CA or name C or name O or name CB )) or resid 62 thro \ ugh 70 or (resid 71 and (name N or name CA or name C or name O or name CB )) or \ resid 72 through 104 or (resid 105 through 107 and (name N or name CA or name C \ or name O or name CB )) or resid 108 through 115 or (resid 116 and (name N or na \ me CA or name C or name O or name CB )) or resid 117 through 128 or (resid 129 t \ hrough 130 and (name N or name CA or name C or name O or name CB )) or resid 131 \ through 148 or (resid 149 and (name N or name CA or name C or name O or name CB \ )) or resid 150 through 161 or (resid 162 and (name N or name CA or name C or n \ ame O or name CB )) or resid 163 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 (res \ id 181 through 182 and (name N or name CA or name C or name O or name CB )) or r \ esid 183 through 194 or resid 207 through 208 or (resid 209 and (name N or name \ CA or name C or name O or name CB )) or resid 210 through 217 or (resid 218 and \ (name N or name CA or name C or name O or name CB )) or resid 219 through 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 226 or (resid 227 through 228 and (name N or name CA or na \ me 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 233 or (resid \ 234 and (name N or name CA or name C or name O or name CB )) or resid 235 throug \ h 238 or (resid 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 (name N or name CA or name C \ or name O or name CB )) or resid 248 through 250 or (resid 251 and (name N or n \ ame CA or name C or name O or name CB )) or resid 252 through 270 or (resid 271 \ and (name N or name CA or name C or name O or name CB )) or resid 272 through 28 \ 1 or (resid 282 through 283 and (name N or name CA or name C or name O or name C \ B )) 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 through 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 name C or name O or name CB )) or resid 31 \ 8 through 325 or (resid 326 and (name N or name CA or name C or name O or name C \ B )) or resid 327 through 335 or (resid 336 and (name N or name CA or name C or \ name O or name CB )) or resid 337 through 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 n \ ame 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 (res \ id 388 through 392 and (name N or name CA or name C or name O or name CB )) or r \ esid 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 399 or (resid 400 through 401 and (name N or na \ me CA or name C or name O or name CB )) or resid 402 through 415 or (resid 416 t \ hrough 420 and (name N or name CA or name C or name O or name CB )) or (resid 42 \ 1 through 430 and (name N or name CA or name C or name O or name CB )) or resid \ 431 through 439 or (resid 440 through 441 and (name N or name CA or name C or na \ me O or name CB )) or resid 442 through 452 or (resid 453 and (name N or name CA \ or name C or name O or name CB )) or resid 454 through 458 or (resid 459 and (n \ ame N or name CA or name C or name O or name CB )) or resid 460 through 469 or ( \ resid 470 through 472 and (name N or name CA or name C or name O or name CB )) o \ r resid 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)) selection = (chain 'D' and (resid 15 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 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 80 or (resid 81 and (name N or name CA or name C or name O or name CB )) or \ resid 82 through 83 or (resid 84 and (name N or name CA or name C or name O or \ name CB )) or resid 85 through 93 or (resid 94 and (name N or name CA or name C \ or name O or name CB )) or resid 95 through 128 or (resid 129 through 130 and (n \ ame N or name CA or name C or name O or name CB )) or resid 131 through 169 or ( \ resid 170 and (name N or name CA or name C or name O or name CB )) or resid 171 \ 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 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 226 or (resid 22 \ 7 through 228 and (name N or name CA or name C or name O or name CB )) or resid \ 229 through 231 or (resid 232 and (name N or name CA or name C or name O or name \ CB )) or resid 233 through 245 or (resid 246 through 247 and (name N or name CA \ or name C or name O or name CB )) or resid 248 through 289 or (resid 290 and (n \ ame N or name CA or name C or name O or name CB )) or resid 291 through 295 or ( \ resid 296 through 297 and (name N or name CA or name C or name O or name CB )) o \ r resid 298 through 316 or (resid 317 and (name N or name CA or name C or name O \ or name CB )) or resid 318 through 335 or (resid 336 and (name N or name CA or \ name C or name O or name CB )) or resid 337 through 384 or (resid 385 through 38 \ 7 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 or (r \ esid 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 (name 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 na \ me C or name O or name CB )) or resid 431 or (resid 432 and (name N or name CA o \ r name C or name O or name CB )) or resid 433 through 439 or (resid 440 through \ 441 and (name N or name CA or name C or name O or name CB )) or resid 442 throug \ h 455 or (resid 456 and (name N or name CA or name C or name O or name CB )) or \ resid 457 through 482 or (resid 483 and (name N or name CA or name C or name O o \ r name CB )) or resid 484 through 485)) selection = (chain 'F' and (resid 15 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 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 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 (r \ esid 40 and (name N or name CA or name C or name O or name CB )) or resid 41 thr \ ough 50 or (resid 51 through 52 and (name N or name CA or name C or name O or na \ me CB )) or resid 53 through 58 or (resid 59 and (name N or name CA or name C or \ name O or name CB )) or resid 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 86 or (resid 87 and (na \ me N or name CA or name C or name O or name CB )) or resid 88 or (resid 89 throu \ gh 90 and (name N or name CA or name C or name O or name CB )) or resid 91 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 98 or (resid 99 and (name N or name CA or name C or name O or na \ me CB )) or resid 100 through 104 or (resid 105 through 107 and (name N or name \ CA or name C or name O or name CB )) or resid 108 through 117 or (resid 118 and \ (name N or name CA or name C or name O or name CB )) or resid 119 through 169 or \ (resid 170 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 1 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 208 or (resid 209 and (name N or name CA o \ r name C or name O or name CB )) or resid 210 through 217 or (resid 218 and (nam \ e N or name CA or name C or name O or name CB )) or resid 219 through 222 or (re \ sid 223 and (name N or name CA or name C or name O or name CB )) or resid 224 th \ rough 227 or (resid 228 and (name N or name CA or name C or name O or name CB )) \ or resid 229 through 233 or (resid 234 and (name N or name CA or name C or name \ O or name CB )) or resid 235 through 238 or (resid 239 and (name N or name CA o \ r name C or name O or name CB )) or resid 240 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 throug \ h 312 or (resid 313 and (name N or name CA or name C or name O or name CB )) or \ resid 314 through 327 or (resid 328 and (name N or name CA or name C or name O o \ r name CB )) or resid 329 through 338 or (resid 339 through 341 and (name N or n \ ame CA or name C or name O or name CB )) or resid 342 through 375 or (resid 376 \ and (name N or name CA or name C or name O or name CB )) or resid 377 through 37 \ 9 or (resid 380 and (name N or name CA or name C or name O or name CB )) or resi \ d 381 through 384 or (resid 385 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 394 or (resid 395 and (name N or na \ me CA or name C or name O or name CB )) or resid 396 through 397 or (resid 398 a \ nd (name N or name CA or name C or name O or name CB )) or resid 399 or (resid 4 \ 00 through 401 and (name N or name CA or name C or name O or name CB )) or resid \ 402 through 431 or (resid 432 and (name N or name CA or name C or name O or nam \ e CB )) or resid 433 through 452 or (resid 453 and (name N or name CA or name C \ or name O or name CB )) or resid 454 through 455 or (resid 456 and (name N or na \ me CA or name C or name O or name CB )) or resid 457 through 458 or (resid 459 a \ nd (name N or name CA or name C or name O or name CB )) or resid 460 through 462 \ or (resid 463 and (name N or name CA or name C or name O or name CB )) or resid \ 464 through 476 or (resid 477 and (name N or name CA or name C or name O or nam \ e CB )) or resid 478 through 485)) } ncs_group { reference = (chain 'G' and ((resid 32 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 101 or (r \ esid 102 through 106 and (name N or name CA or name C or name O or name CB )) or \ resid 107 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 133 or (resid 134 and (name N or \ name CA or name C or name O or name CB )) or resid 135 or (resid 136 through 137 \ and (name N or name CA or name C or name O or name CB )) or resid 138 through 1 \ 41 or (resid 142 through 143 and (name N or name CA or name C or name O or name \ CB )) or resid 144 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 157 or (resid 158 through \ 159 and (name N or name CA or name C or name O or name CB )) or resid 160 throu \ gh 174 or (resid 175 through 178 and (name N or name CA or name C or name O or n \ ame CB )) or resid 179 through 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 197 or (resid 198 and \ (name N or name CA or name C or name O or name CB )) or resid 199 through 204 o \ r (resid 205 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 06 through 229 or (resid 230 through 231 and (name N or name CA or name C or nam \ e O or name CB )))) selection = (chain 'I' and (resid 32 through 102 or (resid 103 through 106 and (name N or na \ me CA or name C or name O or name CB )) or resid 107 through 122 or (resid 123 a \ nd (name N or name CA or name C or name O or name CB )) or resid 124 through 157 \ or (resid 158 through 159 and (name N or name CA or name C or name O or name CB \ )) or resid 160 through 165 or (resid 166 through 167 and (name N or name CA or \ name C or name O or name CB )) or resid 168 through 183 or (resid 184 through 1 \ 85 and (name N or name CA or name C or name O or name CB )) or resid 186 through \ 191 or (resid 192 through 196 and (name N or name CA or name C or name O or nam \ e 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 or (resid 200 and (name N or name CA or name C or name \ O or name CB )) or resid 201 through 210 or (resid 211 through 214 and (name N o \ r name CA or name C or name O or name CB )) or resid 215 through 220 or (resid 2 \ 21 and (name N or name CA or name C or name O or name CB )) or resid 222 through \ 231)) selection = (chain 'K' and ((resid 32 through 85 and (name N or name CA or name C or name O \ or name CB )) or resid 86 or (resid 87 and (name N or name CA or name C or name \ O or name CB )) or resid 88 through 103 or (resid 104 through 106 and (name N or \ name CA or name C or name O or name CB )) or resid 107 through 109 or (resid 11 \ 0 through 116 and (name N or name CA or name C or name O or name CB )) or resid \ 117 or (resid 118 and (name N or name CA or name C or name O or name CB )) or re \ sid 119 through 135 or (resid 136 through 137 and (name N or name CA or name C o \ r name O or name CB )) or resid 138 through 139 or (resid 140 through 143 and (n \ ame N or name CA or name C or name O or name CB )) or resid 144 or (resid 145 th \ rough 148 and (name N or name CA or name C or name O or name CB )) or resid 149 \ through 154 or (resid 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 na \ me O or name CB )) or resid 160 through 175 or (resid 176 through 178 and (name \ N or name CA or name C or name O or name CB )) or resid 179 through 191 or (resi \ d 192 through 196 and (name N or name CA or name C or name O or name CB )) or re \ sid 197 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 32 through 77 and (name N or name CA or name C or name O \ or name CB )) or resid 78 or (resid 79 and (name N or name CA or name C or name \ O or name CB )) or resid 80 through 112)) selection = (chain 'L' and (resid 32 through 95 or (resid 96 and (name N or name CA or name \ C or name O or name CB )) or resid 97 through 99 or (resid 100 and (name N or na \ me CA or name C or name O or name CB )) or resid 101 through 108 or (resid 109 a \ nd (name N or name CA or name C or name O or name CB )) or resid 110 through 112 \ )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.420 Check model and map are aligned: 0.250 Set scattering table: 0.300 Process input model: 74.310 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 : 0.003 0.049 32067 Z= 0.133 Angle : 0.509 9.998 44004 Z= 0.279 Chirality : 0.041 0.226 5489 Planarity : 0.004 0.069 5734 Dihedral : 12.525 142.713 10019 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.87 % Favored : 97.11 % Rotamer: Outliers : 0.18 % Allowed : 0.31 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 1.41 (0.13), residues: 4774 helix: 2.48 (0.11), residues: 2399 sheet: -1.61 (0.24), residues: 474 loop : -0.38 (0.15), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 541 HIS 0.003 0.001 HIS B 344 PHE 0.018 0.001 PHE E 438 TYR 0.016 0.001 TYR B 404 ARG 0.008 0.000 ARG C 370 Details of bonding type rmsd hydrogen bonds : bond 0.16359 ( 2179) hydrogen bonds : angle 6.46814 ( 6423) covalent geometry : bond 0.00294 (32067) covalent geometry : angle 0.50887 (44004) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 442 time to evaluate : 3.299 Fit side-chains REVERT: B 438 LYS cc_start: 0.8048 (mtpt) cc_final: 0.7704 (mttp) REVERT: D 215 MET cc_start: 0.9277 (mtm) cc_final: 0.8987 (mtm) REVERT: E 200 VAL cc_start: 0.8031 (t) cc_final: 0.7796 (m) REVERT: E 370 ARG cc_start: 0.8818 (mtt-85) cc_final: 0.8437 (mtt-85) REVERT: E 513 ILE cc_start: 0.8338 (mt) cc_final: 0.8135 (mt) REVERT: F 357 GLN cc_start: 0.8569 (pm20) cc_final: 0.8250 (pm20) REVERT: K 209 LEU cc_start: 0.8680 (mt) cc_final: 0.8441 (mt) REVERT: K 223 TYR cc_start: 0.8218 (m-80) cc_final: 0.8011 (m-80) outliers start: 4 outliers final: 1 residues processed: 444 average time/residue: 0.4798 time to fit residues: 335.1535 Evaluate side-chains 360 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 359 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 330 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 401 optimal weight: 1.9990 chunk 360 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 242 optimal weight: 4.9990 chunk 192 optimal weight: 0.9980 chunk 372 optimal weight: 30.0000 chunk 144 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 277 optimal weight: 0.9980 chunk 431 optimal weight: 40.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN B 273 HIS ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 122 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.156266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.113623 restraints weight = 41675.459| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.83 r_work: 0.3079 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 32067 Z= 0.323 Angle : 0.627 11.673 44004 Z= 0.328 Chirality : 0.046 0.203 5489 Planarity : 0.005 0.071 5734 Dihedral : 5.830 111.676 5144 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.69 % Favored : 96.29 % Rotamer: Outliers : 1.71 % Allowed : 9.92 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 1.06 (0.13), residues: 4774 helix: 2.28 (0.11), residues: 2396 sheet: -2.02 (0.22), residues: 493 loop : -0.58 (0.14), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 541 HIS 0.006 0.001 HIS A 213 PHE 0.020 0.002 PHE E 438 TYR 0.023 0.002 TYR I 117 ARG 0.007 0.001 ARG E 359 Details of bonding type rmsd hydrogen bonds : bond 0.04960 ( 2179) hydrogen bonds : angle 5.09009 ( 6423) covalent geometry : bond 0.00779 (32067) covalent geometry : angle 0.62659 (44004) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 359 time to evaluate : 11.865 Fit side-chains REVERT: A 312 MET cc_start: 0.9132 (tpt) cc_final: 0.8755 (tpt) REVERT: B 391 MET cc_start: 0.8944 (mtm) cc_final: 0.8570 (mtt) REVERT: B 438 LYS cc_start: 0.8382 (mtpt) cc_final: 0.8122 (mtmm) REVERT: C 191 TYR cc_start: 0.7494 (m-80) cc_final: 0.7013 (m-80) REVERT: C 434 ILE cc_start: 0.8326 (mp) cc_final: 0.8059 (mp) REVERT: D 150 MET cc_start: 0.8881 (ttt) cc_final: 0.8291 (ttt) REVERT: D 215 MET cc_start: 0.9569 (mtm) cc_final: 0.9232 (mtm) REVERT: D 483 GLU cc_start: 0.8179 (tt0) cc_final: 0.7770 (tt0) REVERT: E 100 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8054 (pp) REVERT: E 546 MET cc_start: 0.9031 (mtp) cc_final: 0.8723 (mtp) REVERT: F 32 SER cc_start: 0.9041 (t) cc_final: 0.8778 (t) REVERT: F 228 ASP cc_start: 0.8840 (t0) cc_final: 0.8608 (t0) REVERT: F 339 ASN cc_start: 0.7893 (OUTLIER) cc_final: 0.7677 (t0) REVERT: I 221 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7230 (mm-30) REVERT: K 117 TYR cc_start: 0.8739 (t80) cc_final: 0.8536 (t80) REVERT: M 177 ILE cc_start: 0.8238 (mm) cc_final: 0.7978 (mm) outliers start: 38 outliers final: 27 residues processed: 380 average time/residue: 0.7169 time to fit residues: 449.4576 Evaluate side-chains 364 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 335 time to evaluate : 5.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain F residue 339 ASN Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 36 SER Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 166 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 439 optimal weight: 20.0000 chunk 103 optimal weight: 0.5980 chunk 270 optimal weight: 0.7980 chunk 246 optimal weight: 0.0270 chunk 257 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 289 optimal weight: 0.9980 chunk 312 optimal weight: 7.9990 chunk 178 optimal weight: 0.6980 chunk 266 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 468 ASN E 491 ASN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 446 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 = 0.3902 r_free = 0.3902 target = 0.161847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.120451 restraints weight = 41611.335| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.40 r_work: 0.3174 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32067 Z= 0.138 Angle : 0.481 9.277 44004 Z= 0.252 Chirality : 0.041 0.158 5489 Planarity : 0.004 0.059 5734 Dihedral : 5.409 113.260 5143 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.85 % Favored : 97.13 % Rotamer: Outliers : 1.71 % Allowed : 13.11 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 1.30 (0.13), residues: 4774 helix: 2.50 (0.11), residues: 2402 sheet: -2.03 (0.22), residues: 507 loop : -0.45 (0.15), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 541 HIS 0.002 0.001 HIS B 344 PHE 0.016 0.001 PHE E 438 TYR 0.013 0.001 TYR I 117 ARG 0.006 0.000 ARG C 370 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 2179) hydrogen bonds : angle 4.69651 ( 6423) covalent geometry : bond 0.00312 (32067) covalent geometry : angle 0.48147 (44004) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 398 time to evaluate : 3.874 Fit side-chains revert: symmetry clash REVERT: A 40 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8492 (mtp) REVERT: B 391 MET cc_start: 0.9001 (mtm) cc_final: 0.8626 (mtt) REVERT: B 438 LYS cc_start: 0.8357 (mtpt) cc_final: 0.8093 (mtmm) REVERT: C 191 TYR cc_start: 0.7394 (m-80) cc_final: 0.7050 (m-80) REVERT: C 434 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7744 (mp) REVERT: D 150 MET cc_start: 0.8822 (ttt) cc_final: 0.8266 (ttm) REVERT: D 215 MET cc_start: 0.9493 (mtm) cc_final: 0.9167 (mtm) REVERT: D 395 ASP cc_start: 0.8642 (p0) cc_final: 0.8372 (p0) REVERT: D 483 GLU cc_start: 0.8024 (tt0) cc_final: 0.7671 (tt0) REVERT: E 100 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7928 (pp) REVERT: E 320 ASN cc_start: 0.8651 (t0) cc_final: 0.8404 (t0) REVERT: F 32 SER cc_start: 0.8879 (t) cc_final: 0.8586 (t) REVERT: F 308 MET cc_start: 0.8439 (ttp) cc_final: 0.8140 (ttm) REVERT: I 221 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7150 (mm-30) REVERT: K 117 TYR cc_start: 0.8698 (t80) cc_final: 0.8440 (t80) REVERT: K 215 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8444 (mp) REVERT: M 169 ARG cc_start: 0.8376 (tpt-90) cc_final: 0.8044 (ttt90) outliers start: 38 outliers final: 25 residues processed: 418 average time/residue: 0.4524 time to fit residues: 303.5836 Evaluate side-chains 393 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 364 time to evaluate : 3.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 468 ASN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain J residue 111 ILE Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain L residue 103 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 132 optimal weight: 50.0000 chunk 115 optimal weight: 0.3980 chunk 302 optimal weight: 0.0980 chunk 69 optimal weight: 0.0470 chunk 144 optimal weight: 5.9990 chunk 340 optimal weight: 0.0980 chunk 181 optimal weight: 1.9990 chunk 293 optimal weight: 2.9990 chunk 259 optimal weight: 0.9980 chunk 187 optimal weight: 0.6980 chunk 385 optimal weight: 1.9990 overall best weight: 0.2678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 ASN E 491 ASN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 446 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 = 0.3934 r_free = 0.3934 target = 0.165786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.124572 restraints weight = 41541.251| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.52 r_work: 0.3201 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 32067 Z= 0.109 Angle : 0.461 14.031 44004 Z= 0.239 Chirality : 0.041 0.156 5489 Planarity : 0.003 0.057 5734 Dihedral : 5.232 113.134 5143 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.83 % Favored : 97.15 % Rotamer: Outliers : 2.20 % Allowed : 15.04 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 1.46 (0.13), residues: 4774 helix: 2.62 (0.11), residues: 2406 sheet: -1.86 (0.21), residues: 524 loop : -0.38 (0.15), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 541 HIS 0.002 0.000 HIS B 344 PHE 0.014 0.001 PHE B 439 TYR 0.010 0.001 TYR M 29 ARG 0.006 0.000 ARG G 158 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 2179) hydrogen bonds : angle 4.47909 ( 6423) covalent geometry : bond 0.00232 (32067) covalent geometry : angle 0.46084 (44004) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 407 time to evaluate : 3.575 Fit side-chains revert: symmetry clash REVERT: C 191 TYR cc_start: 0.7274 (m-80) cc_final: 0.7057 (m-80) REVERT: C 434 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7626 (mp) REVERT: D 150 MET cc_start: 0.8706 (ttt) cc_final: 0.8231 (ttm) REVERT: D 215 MET cc_start: 0.9440 (mtm) cc_final: 0.9101 (mtm) REVERT: D 395 ASP cc_start: 0.8557 (p0) cc_final: 0.8283 (p0) REVERT: D 483 GLU cc_start: 0.8061 (tt0) cc_final: 0.7727 (tt0) REVERT: E 100 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7977 (pp) REVERT: F 32 SER cc_start: 0.8832 (t) cc_final: 0.8536 (t) REVERT: F 150 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.7708 (ttt) REVERT: F 395 ASP cc_start: 0.9139 (p0) cc_final: 0.8924 (p0) REVERT: I 152 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.6846 (pmm) REVERT: I 221 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7174 (mm-30) REVERT: K 117 TYR cc_start: 0.8615 (t80) cc_final: 0.8405 (t80) REVERT: K 209 LEU cc_start: 0.8797 (mt) cc_final: 0.8579 (mt) REVERT: M 169 ARG cc_start: 0.8404 (tpt-90) cc_final: 0.8103 (ttt90) outliers start: 49 outliers final: 25 residues processed: 434 average time/residue: 0.4399 time to fit residues: 305.3177 Evaluate side-chains 397 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 368 time to evaluate : 3.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 152 MET Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 111 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain L residue 103 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 325 optimal weight: 0.7980 chunk 451 optimal weight: 50.0000 chunk 8 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 428 optimal weight: 40.0000 chunk 283 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 446 optimal weight: 50.0000 chunk 342 optimal weight: 50.0000 chunk 170 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 446 GLN E 55 ASN F 64 GLN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.157541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.116131 restraints weight = 41889.524| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.55 r_work: 0.3097 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 32067 Z= 0.281 Angle : 0.589 14.784 44004 Z= 0.304 Chirality : 0.045 0.168 5489 Planarity : 0.004 0.052 5734 Dihedral : 5.559 113.647 5143 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.83 % Favored : 96.15 % Rotamer: Outliers : 3.28 % Allowed : 15.81 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 1.22 (0.13), residues: 4774 helix: 2.45 (0.11), residues: 2408 sheet: -2.10 (0.22), residues: 491 loop : -0.54 (0.15), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 541 HIS 0.007 0.001 HIS A 213 PHE 0.016 0.002 PHE A 478 TYR 0.017 0.002 TYR B 407 ARG 0.006 0.001 ARG G 158 Details of bonding type rmsd hydrogen bonds : bond 0.04190 ( 2179) hydrogen bonds : angle 4.67319 ( 6423) covalent geometry : bond 0.00681 (32067) covalent geometry : angle 0.58928 (44004) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 357 time to evaluate : 3.433 Fit side-chains REVERT: A 312 MET cc_start: 0.9070 (tpt) cc_final: 0.8611 (tpt) REVERT: B 391 MET cc_start: 0.9006 (mtm) cc_final: 0.8669 (mtt) REVERT: C 191 TYR cc_start: 0.7789 (m-80) cc_final: 0.7347 (m-80) REVERT: C 434 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7638 (mp) REVERT: D 150 MET cc_start: 0.8880 (ttt) cc_final: 0.8328 (ttm) REVERT: D 215 MET cc_start: 0.9575 (mtm) cc_final: 0.9232 (mtm) REVERT: D 395 ASP cc_start: 0.8842 (p0) cc_final: 0.8570 (p0) REVERT: D 483 GLU cc_start: 0.8131 (tt0) cc_final: 0.7811 (tt0) REVERT: E 100 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8011 (pp) REVERT: E 312 MET cc_start: 0.8989 (tpt) cc_final: 0.8666 (tpt) REVERT: E 432 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8609 (mp) REVERT: F 32 SER cc_start: 0.9019 (t) cc_final: 0.8734 (t) REVERT: I 152 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7285 (pmm) REVERT: I 221 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7246 (mm-30) REVERT: K 117 TYR cc_start: 0.8734 (t80) cc_final: 0.8484 (t80) REVERT: M 177 ILE cc_start: 0.8279 (mm) cc_final: 0.8015 (mm) REVERT: M 192 LEU cc_start: 0.8652 (mt) cc_final: 0.8377 (mp) outliers start: 73 outliers final: 53 residues processed: 401 average time/residue: 0.4289 time to fit residues: 279.5194 Evaluate side-chains 399 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 342 time to evaluate : 3.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 339 ASN Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 152 MET Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain J residue 99 ILE Chi-restraints excluded: chain K residue 104 LYS Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 36 SER Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 166 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 396 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 272 optimal weight: 0.7980 chunk 411 optimal weight: 3.9990 chunk 175 optimal weight: 0.0000 chunk 203 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 439 optimal weight: 9.9990 chunk 383 optimal weight: 1.9990 chunk 327 optimal weight: 0.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 ASN E 468 ASN E 491 ASN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 446 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 = 0.3893 r_free = 0.3893 target = 0.161112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.119875 restraints weight = 41772.443| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.59 r_work: 0.3149 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32067 Z= 0.139 Angle : 0.486 14.304 44004 Z= 0.252 Chirality : 0.041 0.163 5489 Planarity : 0.003 0.053 5734 Dihedral : 5.319 114.486 5143 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.93 % Favored : 97.05 % Rotamer: Outliers : 2.51 % Allowed : 16.88 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 1.37 (0.13), residues: 4774 helix: 2.57 (0.11), residues: 2416 sheet: -1.98 (0.22), residues: 507 loop : -0.48 (0.15), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 541 HIS 0.003 0.001 HIS A 213 PHE 0.014 0.001 PHE E 438 TYR 0.012 0.001 TYR B 49 ARG 0.008 0.000 ARG G 158 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 2179) hydrogen bonds : angle 4.47907 ( 6423) covalent geometry : bond 0.00321 (32067) covalent geometry : angle 0.48609 (44004) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 378 time to evaluate : 3.322 Fit side-chains REVERT: A 40 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8556 (mtp) REVERT: A 126 ARG cc_start: 0.7909 (mtm110) cc_final: 0.7589 (mtp180) REVERT: A 312 MET cc_start: 0.9049 (tpt) cc_final: 0.8461 (tpt) REVERT: A 448 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8523 (ptm160) REVERT: B 391 MET cc_start: 0.9018 (mtm) cc_final: 0.8678 (mtt) REVERT: C 191 TYR cc_start: 0.7724 (m-80) cc_final: 0.7407 (m-80) REVERT: C 434 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7617 (mp) REVERT: D 150 MET cc_start: 0.8753 (ttt) cc_final: 0.8275 (ttm) REVERT: D 215 MET cc_start: 0.9475 (mtm) cc_final: 0.9130 (mtm) REVERT: D 395 ASP cc_start: 0.8683 (p0) cc_final: 0.8417 (p0) REVERT: D 483 GLU cc_start: 0.8105 (tt0) cc_final: 0.7775 (tt0) REVERT: E 100 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7875 (pp) REVERT: E 278 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8145 (mt) REVERT: E 312 MET cc_start: 0.8867 (tpt) cc_final: 0.8660 (tpt) REVERT: F 32 SER cc_start: 0.8881 (t) cc_final: 0.8497 (p) REVERT: F 436 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8359 (tp) REVERT: I 152 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.6940 (pmm) REVERT: I 221 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7192 (mm-30) REVERT: K 117 TYR cc_start: 0.8677 (t80) cc_final: 0.8409 (t80) REVERT: K 209 LEU cc_start: 0.8918 (mt) cc_final: 0.8666 (mt) REVERT: M 192 LEU cc_start: 0.8652 (mt) cc_final: 0.8273 (mp) outliers start: 56 outliers final: 33 residues processed: 414 average time/residue: 0.4466 time to fit residues: 299.4875 Evaluate side-chains 403 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 363 time to evaluate : 3.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 436 LEU Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain I residue 152 MET Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 36 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 234 optimal weight: 5.9990 chunk 275 optimal weight: 0.9990 chunk 423 optimal weight: 50.0000 chunk 96 optimal weight: 0.5980 chunk 199 optimal weight: 0.0370 chunk 162 optimal weight: 50.0000 chunk 358 optimal weight: 0.0170 chunk 334 optimal weight: 20.0000 chunk 188 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 ASN E 491 ASN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 446 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.162652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.121914 restraints weight = 41683.276| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.72 r_work: 0.3187 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32067 Z= 0.120 Angle : 0.467 13.594 44004 Z= 0.242 Chirality : 0.041 0.152 5489 Planarity : 0.003 0.051 5734 Dihedral : 5.213 114.622 5143 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.23 % Favored : 96.75 % Rotamer: Outliers : 2.51 % Allowed : 17.02 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 1.53 (0.13), residues: 4774 helix: 2.70 (0.11), residues: 2407 sheet: -1.87 (0.22), residues: 523 loop : -0.38 (0.15), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 541 HIS 0.003 0.001 HIS B 344 PHE 0.014 0.001 PHE B 439 TYR 0.011 0.001 TYR D 304 ARG 0.007 0.000 ARG G 158 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 2179) hydrogen bonds : angle 4.33536 ( 6423) covalent geometry : bond 0.00273 (32067) covalent geometry : angle 0.46728 (44004) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 391 time to evaluate : 3.805 Fit side-chains revert: symmetry clash REVERT: A 126 ARG cc_start: 0.7893 (mtm110) cc_final: 0.7602 (mtp180) REVERT: A 448 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8456 (ptm160) REVERT: B 391 MET cc_start: 0.8976 (mtm) cc_final: 0.8671 (mtt) REVERT: C 312 MET cc_start: 0.8441 (tpp) cc_final: 0.8032 (mmm) REVERT: C 434 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7541 (mp) REVERT: D 150 MET cc_start: 0.8684 (ttt) cc_final: 0.8210 (ttm) REVERT: D 215 MET cc_start: 0.9404 (mtm) cc_final: 0.9061 (mtm) REVERT: D 468 TYR cc_start: 0.8621 (m-10) cc_final: 0.8398 (m-10) REVERT: D 483 GLU cc_start: 0.8090 (tt0) cc_final: 0.7783 (tt0) REVERT: E 100 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7949 (pp) REVERT: E 278 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8210 (mt) REVERT: E 312 MET cc_start: 0.8862 (tpt) cc_final: 0.8646 (tpt) REVERT: F 395 ASP cc_start: 0.9117 (p0) cc_final: 0.8881 (p0) REVERT: F 436 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8341 (tp) REVERT: I 152 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.6903 (pmm) REVERT: I 166 ARG cc_start: 0.8216 (ptp-110) cc_final: 0.7970 (ptp90) REVERT: I 221 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7206 (mm-30) REVERT: K 117 TYR cc_start: 0.8661 (t80) cc_final: 0.8391 (t80) outliers start: 56 outliers final: 38 residues processed: 426 average time/residue: 0.6560 time to fit residues: 454.6898 Evaluate side-chains 409 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 365 time to evaluate : 8.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 436 LEU Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain I residue 152 MET Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain K residue 104 LYS Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 36 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 73 optimal weight: 0.9990 chunk 356 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 392 optimal weight: 10.0000 chunk 211 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 280 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 207 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 ASN E 491 ASN F 64 GLN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 HIS ** 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 = 0.3886 r_free = 0.3886 target = 0.160522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.118610 restraints weight = 41817.418| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.22 r_work: 0.3149 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 32067 Z= 0.174 Angle : 0.512 16.118 44004 Z= 0.262 Chirality : 0.042 0.159 5489 Planarity : 0.004 0.049 5734 Dihedral : 5.321 115.199 5143 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.50 % Favored : 96.48 % Rotamer: Outliers : 2.56 % Allowed : 17.56 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 1.48 (0.13), residues: 4774 helix: 2.66 (0.11), residues: 2407 sheet: -1.93 (0.22), residues: 501 loop : -0.40 (0.15), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 541 HIS 0.005 0.001 HIS A 213 PHE 0.013 0.001 PHE B 439 TYR 0.015 0.001 TYR F 352 ARG 0.008 0.000 ARG G 158 Details of bonding type rmsd hydrogen bonds : bond 0.03647 ( 2179) hydrogen bonds : angle 4.39483 ( 6423) covalent geometry : bond 0.00414 (32067) covalent geometry : angle 0.51169 (44004) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 370 time to evaluate : 3.502 Fit side-chains revert: symmetry clash REVERT: A 126 ARG cc_start: 0.7904 (mtm110) cc_final: 0.7607 (mtp180) REVERT: A 481 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8429 (mp) REVERT: B 391 MET cc_start: 0.9019 (mtm) cc_final: 0.8689 (mtt) REVERT: C 434 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7597 (mp) REVERT: D 150 MET cc_start: 0.8748 (ttt) cc_final: 0.8228 (ttm) REVERT: D 215 MET cc_start: 0.9454 (mtm) cc_final: 0.9108 (mtm) REVERT: D 395 ASP cc_start: 0.8705 (p0) cc_final: 0.8444 (p0) REVERT: D 483 GLU cc_start: 0.8094 (tt0) cc_final: 0.7792 (tt0) REVERT: E 100 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8009 (pp) REVERT: E 278 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8231 (mt) REVERT: E 312 MET cc_start: 0.8992 (tpt) cc_final: 0.8715 (tpt) REVERT: F 32 SER cc_start: 0.8917 (t) cc_final: 0.8627 (t) REVERT: F 395 ASP cc_start: 0.9160 (p0) cc_final: 0.8937 (p0) REVERT: F 436 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8366 (tp) REVERT: I 152 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.7114 (pmm) REVERT: I 166 ARG cc_start: 0.8175 (ptp-110) cc_final: 0.7935 (ptp90) REVERT: I 221 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7231 (mm-30) REVERT: K 117 TYR cc_start: 0.8729 (t80) cc_final: 0.8512 (t80) outliers start: 57 outliers final: 45 residues processed: 404 average time/residue: 0.4429 time to fit residues: 286.3179 Evaluate side-chains 415 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 364 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 468 ASN Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 468 ASN Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 436 LEU Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain I residue 152 MET Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 104 LYS Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain L residue 96 LYS Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 36 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 139 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 146 optimal weight: 30.0000 chunk 313 optimal weight: 50.0000 chunk 37 optimal weight: 4.9990 chunk 432 optimal weight: 10.0000 chunk 344 optimal weight: 7.9990 chunk 283 optimal weight: 0.9990 chunk 239 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 ASN E 491 ASN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 HIS ** 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 = 0.3853 r_free = 0.3853 target = 0.157542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.116523 restraints weight = 41950.246| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.69 r_work: 0.3096 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 32067 Z= 0.255 Angle : 0.576 15.904 44004 Z= 0.296 Chirality : 0.044 0.163 5489 Planarity : 0.004 0.060 5734 Dihedral : 5.553 116.797 5143 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.90 % Favored : 96.08 % Rotamer: Outliers : 3.10 % Allowed : 16.97 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 1.25 (0.13), residues: 4774 helix: 2.51 (0.11), residues: 2406 sheet: -2.10 (0.22), residues: 511 loop : -0.54 (0.15), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 541 HIS 0.006 0.001 HIS A 213 PHE 0.026 0.002 PHE B 241 TYR 0.017 0.002 TYR F 352 ARG 0.010 0.001 ARG G 158 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 2179) hydrogen bonds : angle 4.55728 ( 6423) covalent geometry : bond 0.00616 (32067) covalent geometry : angle 0.57627 (44004) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 356 time to evaluate : 3.734 Fit side-chains revert: symmetry clash REVERT: A 126 ARG cc_start: 0.7986 (mtm110) cc_final: 0.7694 (mtp180) REVERT: A 378 GLN cc_start: 0.9219 (tt0) cc_final: 0.8969 (tt0) REVERT: B 383 MET cc_start: 0.8558 (ttt) cc_final: 0.8219 (ttt) REVERT: B 391 MET cc_start: 0.8999 (mtm) cc_final: 0.8595 (mtt) REVERT: C 434 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7571 (mp) REVERT: D 150 MET cc_start: 0.8860 (ttt) cc_final: 0.8305 (ttm) REVERT: D 215 MET cc_start: 0.9524 (mtm) cc_final: 0.9189 (mtm) REVERT: D 226 LYS cc_start: 0.8355 (ttmm) cc_final: 0.8153 (mttm) REVERT: D 483 GLU cc_start: 0.8106 (tt0) cc_final: 0.7792 (tt0) REVERT: E 100 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8023 (pp) REVERT: E 312 MET cc_start: 0.9046 (tpt) cc_final: 0.8687 (tpt) REVERT: F 32 SER cc_start: 0.9012 (t) cc_final: 0.8702 (t) REVERT: I 152 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.7223 (pmm) REVERT: I 221 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7249 (mm-30) REVERT: K 117 TYR cc_start: 0.8735 (t80) cc_final: 0.8520 (t80) REVERT: M 177 ILE cc_start: 0.8114 (mm) cc_final: 0.7857 (mm) outliers start: 69 outliers final: 55 residues processed: 399 average time/residue: 0.5998 time to fit residues: 390.9953 Evaluate side-chains 408 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 350 time to evaluate : 4.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 468 ASN Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 468 ASN Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 172 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 152 MET Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 104 LYS Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 36 SER Chi-restraints excluded: chain M residue 166 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 187 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 195 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 227 optimal weight: 0.6980 chunk 306 optimal weight: 20.0000 chunk 311 optimal weight: 0.0670 chunk 21 optimal weight: 0.1980 chunk 201 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 GLN ** D 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 ASN E 491 ASN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 HIS ** 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 = 0.3903 r_free = 0.3903 target = 0.161785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.120648 restraints weight = 41703.050| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.50 r_work: 0.3140 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32067 Z= 0.129 Angle : 0.493 15.245 44004 Z= 0.253 Chirality : 0.041 0.154 5489 Planarity : 0.004 0.062 5734 Dihedral : 5.303 115.174 5143 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.12 % Favored : 96.86 % Rotamer: Outliers : 2.51 % Allowed : 17.69 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 1.41 (0.13), residues: 4774 helix: 2.60 (0.11), residues: 2423 sheet: -1.94 (0.22), residues: 499 loop : -0.47 (0.15), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 541 HIS 0.003 0.001 HIS A 213 PHE 0.015 0.001 PHE F 439 TYR 0.025 0.001 TYR I 117 ARG 0.011 0.000 ARG E 359 Details of bonding type rmsd hydrogen bonds : bond 0.03505 ( 2179) hydrogen bonds : angle 4.37569 ( 6423) covalent geometry : bond 0.00294 (32067) covalent geometry : angle 0.49346 (44004) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 380 time to evaluate : 3.711 Fit side-chains revert: symmetry clash REVERT: A 378 GLN cc_start: 0.9286 (tt0) cc_final: 0.9006 (tt0) REVERT: A 481 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8426 (mp) REVERT: B 391 MET cc_start: 0.9034 (mtm) cc_final: 0.8644 (mtt) REVERT: C 434 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7567 (mp) REVERT: D 150 MET cc_start: 0.8664 (ttt) cc_final: 0.8172 (ttm) REVERT: D 215 MET cc_start: 0.9390 (mtm) cc_final: 0.9068 (mtm) REVERT: D 483 GLU cc_start: 0.8022 (tt0) cc_final: 0.7700 (tt0) REVERT: E 100 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8040 (pp) REVERT: E 312 MET cc_start: 0.8957 (tpt) cc_final: 0.8654 (tpt) REVERT: F 32 SER cc_start: 0.8910 (t) cc_final: 0.8611 (t) REVERT: F 395 ASP cc_start: 0.9140 (p0) cc_final: 0.8933 (p0) REVERT: I 152 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.6933 (pmm) REVERT: I 166 ARG cc_start: 0.8265 (ptp-110) cc_final: 0.8012 (ptp90) REVERT: I 221 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7286 (mm-30) REVERT: K 87 LYS cc_start: 0.9121 (tttt) cc_final: 0.8897 (tttt) REVERT: K 106 LYS cc_start: 0.8939 (mtpp) cc_final: 0.8574 (mtmm) REVERT: K 117 TYR cc_start: 0.8714 (t80) cc_final: 0.8471 (t80) REVERT: K 122 GLN cc_start: 0.8664 (tp40) cc_final: 0.7650 (tp40) outliers start: 56 outliers final: 46 residues processed: 414 average time/residue: 0.4406 time to fit residues: 292.0095 Evaluate side-chains 418 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 368 time to evaluate : 3.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 527 GLN Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 468 ASN Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 468 ASN Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain I residue 152 MET Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 36 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 296 optimal weight: 2.9990 chunk 292 optimal weight: 0.6980 chunk 318 optimal weight: 0.6980 chunk 374 optimal weight: 50.0000 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 440 optimal weight: 10.0000 chunk 285 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 460 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 GLN ** D 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 ASN E 491 ASN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 HIS ** 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 = 0.3895 r_free = 0.3895 target = 0.161140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.119703 restraints weight = 41580.294| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.53 r_work: 0.3116 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32067 Z= 0.158 Angle : 0.513 15.289 44004 Z= 0.262 Chirality : 0.042 0.153 5489 Planarity : 0.004 0.052 5734 Dihedral : 5.313 114.861 5143 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.46 % Favored : 96.52 % Rotamer: Outliers : 2.56 % Allowed : 17.60 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 1.42 (0.13), residues: 4774 helix: 2.60 (0.11), residues: 2422 sheet: -1.90 (0.22), residues: 502 loop : -0.46 (0.15), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 541 HIS 0.004 0.001 HIS A 213 PHE 0.014 0.001 PHE B 241 TYR 0.047 0.001 TYR F 352 ARG 0.009 0.000 ARG G 158 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 2179) hydrogen bonds : angle 4.37457 ( 6423) covalent geometry : bond 0.00374 (32067) covalent geometry : angle 0.51302 (44004) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20938.23 seconds wall clock time: 370 minutes 46.87 seconds (22246.87 seconds total)