Starting phenix.real_space_refine on Fri Feb 6 09:22:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nud_49801/02_2026/9nud_49801_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nud_49801/02_2026/9nud_49801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nud_49801/02_2026/9nud_49801_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nud_49801/02_2026/9nud_49801_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nud_49801/02_2026/9nud_49801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nud_49801/02_2026/9nud_49801.map" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.077 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 30 5.49 5 Mg 6 5.21 5 S 107 5.16 5 C 14791 2.51 5 N 4080 2.21 5 O 4649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 193 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23663 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3867 Classifications: {'peptide': 497} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 476} Chain breaks: 2 Chain: "B" Number of atoms: 3907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3907 Classifications: {'peptide': 502} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 481} Chain breaks: 2 Chain: "C" Number of atoms: 3907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3907 Classifications: {'peptide': 502} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 481} Chain breaks: 2 Chain: "D" Number of atoms: 3907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3907 Classifications: {'peptide': 502} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 481} Chain breaks: 2 Chain: "E" Number of atoms: 3907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3907 Classifications: {'peptide': 502} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 481} Chain breaks: 2 Chain: "F" Number of atoms: 3769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3769 Classifications: {'peptide': 482} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 461} Chain breaks: 4 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 5.38, per 1000 atoms: 0.23 Number of scatterers: 23663 At special positions: 0 Unit cell: (158.279, 127.014, 158.279, 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 107 16.00 P 30 15.00 Mg 6 11.99 O 4649 8.00 N 4080 7.00 C 14791 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: 1.80 Conformation dependent library (CDL) restraints added in 919.2 milliseconds 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5612 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 12 sheets defined 61.2% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 244 through 256 removed outlier: 4.072A pdb=" N THR A 249 " --> pdb=" O ASP A 245 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 270 Processing helix chain 'A' and resid 286 through 298 removed outlier: 4.004A pdb=" N ILE A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 291 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 315 through 322 removed outlier: 3.519A pdb=" N ASN A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 326 Processing helix chain 'A' and resid 327 through 338 Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.768A pdb=" N VAL A 354 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 381 removed outlier: 3.517A pdb=" N LYS A 378 " --> pdb=" O GLN A 374 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET A 379 " --> pdb=" O LEU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 401 through 405 Processing helix chain 'A' and resid 420 through 432 Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 446 through 454 removed outlier: 3.932A pdb=" N LEU A 450 " --> pdb=" O ASN A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 476 removed outlier: 3.558A pdb=" N LYS A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 509 removed outlier: 4.573A pdb=" N LEU A 506 " --> pdb=" O PHE A 502 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 525 removed outlier: 4.227A pdb=" N CYS A 523 " --> pdb=" O ASP A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 552 removed outlier: 3.698A pdb=" N ASN A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG A 544 " --> pdb=" O LYS A 540 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR A 545 " --> pdb=" O ASN A 541 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 546 " --> pdb=" O GLY A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 580 removed outlier: 3.646A pdb=" N ALA A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 580 " --> pdb=" O GLU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 614 removed outlier: 3.593A pdb=" N ALA A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 630 Processing helix chain 'A' and resid 640 through 651 Processing helix chain 'A' and resid 669 through 677 Processing helix chain 'A' and resid 693 through 704 Processing helix chain 'A' and resid 708 through 723 removed outlier: 4.137A pdb=" N LYS A 714 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG A 721 " --> pdb=" O ASN A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 742 removed outlier: 3.737A pdb=" N HIS A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 758 Processing helix chain 'B' and resid 244 through 256 removed outlier: 4.004A pdb=" N LYS B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 256 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 261 removed outlier: 3.765A pdb=" N ILE B 260 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 256 through 261' Processing helix chain 'B' and resid 262 through 270 removed outlier: 3.544A pdb=" N ILE B 266 " --> pdb=" O PRO B 262 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS B 268 " --> pdb=" O SER B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 removed outlier: 3.726A pdb=" N ILE B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR B 296 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 298 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 315 through 338 removed outlier: 4.087A pdb=" N ILE B 323 " --> pdb=" O SER B 319 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ARG B 324 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS B 328 " --> pdb=" O ARG B 324 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASP B 329 " --> pdb=" O ASN B 325 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ALA B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU B 333 " --> pdb=" O ASP B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 350 through 356 removed outlier: 3.744A pdb=" N VAL B 354 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 378 Processing helix chain 'B' and resid 401 through 405 Processing helix chain 'B' and resid 420 through 437 removed outlier: 3.671A pdb=" N LEU B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LYS B 434 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N MET B 435 " --> pdb=" O GLN B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 454 removed outlier: 3.539A pdb=" N LEU B 450 " --> pdb=" O ASN B 446 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 476 removed outlier: 3.568A pdb=" N GLY B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA B 473 " --> pdb=" O ALA B 469 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 505 Processing helix chain 'B' and resid 506 through 508 No H-bonds generated for 'chain 'B' and resid 506 through 508' Processing helix chain 'B' and resid 516 through 522 removed outlier: 3.748A pdb=" N THR B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 552 removed outlier: 3.708A pdb=" N ASN B 536 " --> pdb=" O SER B 532 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG B 544 " --> pdb=" O LYS B 540 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR B 545 " --> pdb=" O ASN B 541 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 546 " --> pdb=" O GLY B 542 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG B 547 " --> pdb=" O ALA B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 580 removed outlier: 3.801A pdb=" N LEU B 573 " --> pdb=" O GLY B 569 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B 580 " --> pdb=" O GLU B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 614 removed outlier: 3.903A pdb=" N ALA B 604 " --> pdb=" O SER B 600 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR B 614 " --> pdb=" O PHE B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 630 removed outlier: 3.573A pdb=" N LEU B 629 " --> pdb=" O SER B 625 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 625 through 630' Processing helix chain 'B' and resid 640 through 651 removed outlier: 3.669A pdb=" N VAL B 649 " --> pdb=" O GLN B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 674 Processing helix chain 'B' and resid 693 through 704 Processing helix chain 'B' and resid 708 through 723 removed outlier: 4.600A pdb=" N LYS B 714 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL B 715 " --> pdb=" O GLY B 711 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE B 716 " --> pdb=" O ARG B 712 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG B 721 " --> pdb=" O ASN B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 741 removed outlier: 3.509A pdb=" N THR B 735 " --> pdb=" O LYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 758 removed outlier: 4.027A pdb=" N VAL B 751 " --> pdb=" O VAL B 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 256 removed outlier: 3.686A pdb=" N PHE C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG C 254 " --> pdb=" O LYS C 250 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE C 256 " --> pdb=" O PHE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 261 removed outlier: 3.622A pdb=" N ILE C 260 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 256 through 261' Processing helix chain 'C' and resid 262 through 270 Processing helix chain 'C' and resid 286 through 299 removed outlier: 3.651A pdb=" N ALA C 291 " --> pdb=" O LYS C 287 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR C 296 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N MET C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 298 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 314 Processing helix chain 'C' and resid 315 through 338 removed outlier: 4.861A pdb=" N GLU C 321 " --> pdb=" O GLY C 317 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE C 323 " --> pdb=" O SER C 319 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ARG C 324 " --> pdb=" O GLU C 320 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ASP C 329 " --> pdb=" O ASN C 325 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ALA C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA C 332 " --> pdb=" O LYS C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 341 No H-bonds generated for 'chain 'C' and resid 339 through 341' Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.959A pdb=" N VAL C 354 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 380 removed outlier: 3.753A pdb=" N LYS C 378 " --> pdb=" O GLN C 374 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET C 379 " --> pdb=" O LEU C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 405 Processing helix chain 'C' and resid 420 through 437 removed outlier: 3.612A pdb=" N LEU C 425 " --> pdb=" O GLU C 421 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLN C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LYS C 434 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N MET C 435 " --> pdb=" O GLN C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 454 removed outlier: 3.523A pdb=" N LEU C 450 " --> pdb=" O ASN C 446 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA C 452 " --> pdb=" O ALA C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 478 removed outlier: 3.745A pdb=" N ILE C 462 " --> pdb=" O SER C 458 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU C 463 " --> pdb=" O GLY C 459 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE C 472 " --> pdb=" O SER C 468 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA C 473 " --> pdb=" O ALA C 469 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR C 477 " --> pdb=" O ALA C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 495 Processing helix chain 'C' and resid 500 through 505 Processing helix chain 'C' and resid 506 through 508 No H-bonds generated for 'chain 'C' and resid 506 through 508' Processing helix chain 'C' and resid 516 through 522 removed outlier: 3.746A pdb=" N LEU C 520 " --> pdb=" O SER C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 552 removed outlier: 3.571A pdb=" N LEU C 539 " --> pdb=" O VAL C 535 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS C 540 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG C 544 " --> pdb=" O LYS C 540 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG C 547 " --> pdb=" O ALA C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 580 removed outlier: 3.659A pdb=" N LEU C 573 " --> pdb=" O GLY C 569 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS C 580 " --> pdb=" O GLU C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 595 removed outlier: 3.776A pdb=" N LEU C 594 " --> pdb=" O SER C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 614 removed outlier: 3.743A pdb=" N ALA C 604 " --> pdb=" O SER C 600 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP C 612 " --> pdb=" O ASN C 608 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR C 614 " --> pdb=" O PHE C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 630 removed outlier: 3.557A pdb=" N LEU C 629 " --> pdb=" O SER C 625 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL C 630 " --> pdb=" O LEU C 626 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 625 through 630' Processing helix chain 'C' and resid 640 through 651 removed outlier: 3.594A pdb=" N LEU C 644 " --> pdb=" O SER C 640 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN C 645 " --> pdb=" O ASN C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 676 removed outlier: 3.515A pdb=" N LEU C 673 " --> pdb=" O ALA C 669 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN C 675 " --> pdb=" O SER C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 677 through 681 removed outlier: 4.075A pdb=" N SER C 680 " --> pdb=" O ASP C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 704 removed outlier: 3.903A pdb=" N LEU C 697 " --> pdb=" O ASN C 693 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN C 698 " --> pdb=" O LEU C 694 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN C 699 " --> pdb=" O ASP C 695 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 700 " --> pdb=" O GLU C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 721 removed outlier: 3.913A pdb=" N LYS C 714 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG C 721 " --> pdb=" O ASN C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 741 removed outlier: 3.688A pdb=" N THR C 735 " --> pdb=" O LYS C 731 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 738 " --> pdb=" O LEU C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 758 removed outlier: 3.804A pdb=" N VAL C 751 " --> pdb=" O VAL C 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 256 removed outlier: 3.536A pdb=" N THR D 249 " --> pdb=" O ASP D 245 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS D 250 " --> pdb=" O LYS D 246 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG D 254 " --> pdb=" O LYS D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 261 removed outlier: 3.516A pdb=" N ILE D 260 " --> pdb=" O PHE D 256 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 256 through 261' Processing helix chain 'D' and resid 262 through 270 removed outlier: 3.602A pdb=" N ILE D 266 " --> pdb=" O PRO D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 298 removed outlier: 3.535A pdb=" N ALA D 291 " --> pdb=" O LYS D 287 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY D 295 " --> pdb=" O ALA D 291 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU D 298 " --> pdb=" O ILE D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 Processing helix chain 'D' and resid 315 through 327 removed outlier: 3.701A pdb=" N ILE D 323 " --> pdb=" O SER D 319 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG D 324 " --> pdb=" O GLU D 320 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 338 Processing helix chain 'D' and resid 339 through 341 No H-bonds generated for 'chain 'D' and resid 339 through 341' Processing helix chain 'D' and resid 351 through 356 removed outlier: 4.266A pdb=" N PHE D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS D 356 " --> pdb=" O ASP D 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 351 through 356' Processing helix chain 'D' and resid 369 through 381 removed outlier: 3.777A pdb=" N MET D 379 " --> pdb=" O LEU D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 400 Processing helix chain 'D' and resid 401 through 405 Processing helix chain 'D' and resid 420 through 432 removed outlier: 3.633A pdb=" N LEU D 425 " --> pdb=" O GLU D 421 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN D 426 " --> pdb=" O LYS D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 438 Processing helix chain 'D' and resid 446 through 454 removed outlier: 4.282A pdb=" N ALA D 452 " --> pdb=" O ALA D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 476 removed outlier: 3.804A pdb=" N GLU D 463 " --> pdb=" O GLY D 459 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY D 464 " --> pdb=" O ALA D 460 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE D 472 " --> pdb=" O SER D 468 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA D 473 " --> pdb=" O ALA D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 495 Processing helix chain 'D' and resid 498 through 509 removed outlier: 3.513A pdb=" N PHE D 502 " --> pdb=" O THR D 498 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASN D 507 " --> pdb=" O LEU D 503 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP D 508 " --> pdb=" O ASN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 525 removed outlier: 4.287A pdb=" N CYS D 523 " --> pdb=" O ASP D 519 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU D 525 " --> pdb=" O LYS D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 552 removed outlier: 3.827A pdb=" N ASN D 536 " --> pdb=" O SER D 532 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER D 537 " --> pdb=" O GLU D 533 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR D 545 " --> pdb=" O ASN D 541 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL D 546 " --> pdb=" O GLY D 542 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG D 547 " --> pdb=" O ALA D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 579 removed outlier: 3.598A pdb=" N LEU D 573 " --> pdb=" O GLY D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 595 removed outlier: 3.756A pdb=" N LEU D 594 " --> pdb=" O SER D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 613 removed outlier: 3.917A pdb=" N ALA D 604 " --> pdb=" O SER D 600 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA D 613 " --> pdb=" O THR D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 616 No H-bonds generated for 'chain 'D' and resid 614 through 616' Processing helix chain 'D' and resid 625 through 630 removed outlier: 3.752A pdb=" N VAL D 630 " --> pdb=" O LEU D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 651 removed outlier: 3.563A pdb=" N LEU D 644 " --> pdb=" O SER D 640 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL D 649 " --> pdb=" O GLN D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 677 removed outlier: 4.187A pdb=" N GLN D 675 " --> pdb=" O SER D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 682 removed outlier: 3.841A pdb=" N PHE D 682 " --> pdb=" O LEU D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 704 removed outlier: 3.596A pdb=" N SER D 704 " --> pdb=" O VAL D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 723 removed outlier: 4.827A pdb=" N LYS D 714 " --> pdb=" O ALA D 710 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL D 715 " --> pdb=" O GLY D 711 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE D 716 " --> pdb=" O ARG D 712 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG D 721 " --> pdb=" O ASN D 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 742 removed outlier: 4.284A pdb=" N HIS D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 745 through 758 Processing helix chain 'E' and resid 244 through 256 removed outlier: 3.571A pdb=" N THR E 249 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS E 250 " --> pdb=" O LYS E 246 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE E 251 " --> pdb=" O GLU E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 261 removed outlier: 3.638A pdb=" N ILE E 260 " --> pdb=" O PHE E 256 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N PHE E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 256 through 261' Processing helix chain 'E' and resid 262 through 270 Processing helix chain 'E' and resid 286 through 298 removed outlier: 3.542A pdb=" N ILE E 290 " --> pdb=" O GLY E 286 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY E 295 " --> pdb=" O ALA E 291 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR E 296 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET E 297 " --> pdb=" O LYS E 293 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU E 298 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 314 Processing helix chain 'E' and resid 315 through 327 removed outlier: 3.566A pdb=" N ILE E 323 " --> pdb=" O SER E 319 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG E 324 " --> pdb=" O GLU E 320 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE E 327 " --> pdb=" O ILE E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 338 removed outlier: 3.632A pdb=" N TYR E 334 " --> pdb=" O ALA E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 341 No H-bonds generated for 'chain 'E' and resid 339 through 341' Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.540A pdb=" N VAL E 354 " --> pdb=" O LEU E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 381 removed outlier: 3.940A pdb=" N MET E 379 " --> pdb=" O LEU E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 405 Processing helix chain 'E' and resid 420 through 432 removed outlier: 3.610A pdb=" N LEU E 425 " --> pdb=" O GLU E 421 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN E 426 " --> pdb=" O LYS E 422 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP E 429 " --> pdb=" O LEU E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 438 removed outlier: 3.618A pdb=" N ASN E 438 " --> pdb=" O LYS E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 454 removed outlier: 3.747A pdb=" N LEU E 450 " --> pdb=" O ASN E 446 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA E 452 " --> pdb=" O ALA E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 478 removed outlier: 3.987A pdb=" N GLU E 463 " --> pdb=" O GLY E 459 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY E 464 " --> pdb=" O ALA E 460 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE E 472 " --> pdb=" O SER E 468 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA E 473 " --> pdb=" O ALA E 469 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE E 474 " --> pdb=" O SER E 470 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR E 477 " --> pdb=" O ALA E 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 491 through 495 removed outlier: 4.012A pdb=" N LEU E 495 " --> pdb=" O ILE E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 505 Processing helix chain 'E' and resid 506 through 508 No H-bonds generated for 'chain 'E' and resid 506 through 508' Processing helix chain 'E' and resid 520 through 525 Processing helix chain 'E' and resid 532 through 551 removed outlier: 3.790A pdb=" N ASN E 536 " --> pdb=" O SER E 532 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR E 545 " --> pdb=" O ASN E 541 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL E 546 " --> pdb=" O GLY E 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 580 removed outlier: 3.719A pdb=" N LEU E 573 " --> pdb=" O GLY E 569 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA E 578 " --> pdb=" O ALA E 574 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS E 580 " --> pdb=" O GLU E 576 " (cutoff:3.500A) Processing helix chain 'E' and resid 590 through 595 removed outlier: 3.822A pdb=" N LEU E 594 " --> pdb=" O SER E 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 614 removed outlier: 3.833A pdb=" N ALA E 604 " --> pdb=" O SER E 600 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR E 614 " --> pdb=" O PHE E 610 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 630 removed outlier: 3.565A pdb=" N LEU E 629 " --> pdb=" O SER E 625 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL E 630 " --> pdb=" O LEU E 626 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 625 through 630' Processing helix chain 'E' and resid 640 through 651 removed outlier: 3.591A pdb=" N LEU E 644 " --> pdb=" O SER E 640 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL E 649 " --> pdb=" O GLN E 645 " (cutoff:3.500A) Processing helix chain 'E' and resid 669 through 676 Processing helix chain 'E' and resid 677 through 681 removed outlier: 3.814A pdb=" N SER E 680 " --> pdb=" O ASP E 677 " (cutoff:3.500A) Processing helix chain 'E' and resid 693 through 704 removed outlier: 3.521A pdb=" N LEU E 697 " --> pdb=" O ASN E 693 " (cutoff:3.500A) Processing helix chain 'E' and resid 708 through 723 removed outlier: 3.648A pdb=" N ARG E 712 " --> pdb=" O ASP E 708 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS E 714 " --> pdb=" O ALA E 710 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG E 721 " --> pdb=" O ASN E 717 " (cutoff:3.500A) Processing helix chain 'E' and resid 729 through 741 removed outlier: 3.560A pdb=" N THR E 735 " --> pdb=" O LYS E 731 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU E 738 " --> pdb=" O LEU E 734 " (cutoff:3.500A) Processing helix chain 'E' and resid 745 through 758 removed outlier: 4.121A pdb=" N VAL E 751 " --> pdb=" O VAL E 747 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU E 752 " --> pdb=" O ASN E 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 256 removed outlier: 3.503A pdb=" N ILE F 251 " --> pdb=" O GLU F 247 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG F 253 " --> pdb=" O THR F 249 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG F 254 " --> pdb=" O LYS F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 261 removed outlier: 3.804A pdb=" N PHE F 261 " --> pdb=" O ALA F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 267 Processing helix chain 'F' and resid 286 through 292 removed outlier: 3.688A pdb=" N ILE F 290 " --> pdb=" O GLY F 286 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA F 291 " --> pdb=" O LYS F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 313 Processing helix chain 'F' and resid 315 through 322 Processing helix chain 'F' and resid 322 through 336 removed outlier: 3.688A pdb=" N PHE F 327 " --> pdb=" O ILE F 323 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASP F 329 " --> pdb=" O ASN F 325 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ALA F 330 " --> pdb=" O LEU F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 355 Processing helix chain 'F' and resid 369 through 378 Processing helix chain 'F' and resid 396 through 400 Processing helix chain 'F' and resid 401 through 405 Processing helix chain 'F' and resid 420 through 432 Processing helix chain 'F' and resid 432 through 438 removed outlier: 3.519A pdb=" N GLU F 437 " --> pdb=" O LYS F 433 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN F 438 " --> pdb=" O LYS F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 454 removed outlier: 3.692A pdb=" N LEU F 450 " --> pdb=" O ASN F 446 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA F 451 " --> pdb=" O LEU F 447 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA F 452 " --> pdb=" O ALA F 448 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU F 453 " --> pdb=" O GLU F 449 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR F 454 " --> pdb=" O LEU F 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 446 through 454' Processing helix chain 'F' and resid 460 through 476 removed outlier: 3.572A pdb=" N GLY F 464 " --> pdb=" O ALA F 460 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL F 466 " --> pdb=" O ILE F 462 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE F 472 " --> pdb=" O SER F 468 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA F 473 " --> pdb=" O ALA F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 491 through 495 removed outlier: 3.712A pdb=" N LYS F 494 " --> pdb=" O ASP F 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 500 through 509 removed outlier: 4.813A pdb=" N LEU F 506 " --> pdb=" O PHE F 502 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASN F 507 " --> pdb=" O LEU F 503 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP F 508 " --> pdb=" O ASN F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 516 through 523 removed outlier: 3.569A pdb=" N LEU F 520 " --> pdb=" O SER F 516 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS F 523 " --> pdb=" O ASP F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 552 removed outlier: 3.972A pdb=" N ASN F 536 " --> pdb=" O SER F 532 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG F 544 " --> pdb=" O LYS F 540 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR F 545 " --> pdb=" O ASN F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 580 Processing helix chain 'F' and resid 590 through 595 removed outlier: 3.932A pdb=" N LEU F 594 " --> pdb=" O SER F 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 614 removed outlier: 3.551A pdb=" N TYR F 614 " --> pdb=" O PHE F 610 " (cutoff:3.500A) Processing helix chain 'F' and resid 625 through 630 Processing helix chain 'F' and resid 640 through 651 removed outlier: 3.526A pdb=" N LEU F 644 " --> pdb=" O SER F 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 669 through 677 Processing helix chain 'F' and resid 678 through 682 removed outlier: 3.732A pdb=" N PHE F 682 " --> pdb=" O LEU F 679 " (cutoff:3.500A) Processing helix chain 'F' and resid 693 through 704 Processing helix chain 'F' and resid 708 through 723 removed outlier: 4.136A pdb=" N LYS F 714 " --> pdb=" O ALA F 710 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG F 721 " --> pdb=" O ASN F 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 729 through 742 removed outlier: 3.960A pdb=" N HIS F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 745 through 758 removed outlier: 3.509A pdb=" N VAL F 751 " --> pdb=" O VAL F 747 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 304 through 307 removed outlier: 6.342A pdb=" N LYS A 304 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ASP A 349 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 306 " --> pdb=" O ASP A 349 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL A 412 " --> pdb=" O GLY A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 585 through 589 removed outlier: 3.539A pdb=" N ARG A 587 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 558 " --> pdb=" O LEU A 661 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN A 684 " --> pdb=" O SER A 559 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 304 through 307 removed outlier: 6.778A pdb=" N LYS B 304 " --> pdb=" O ILE B 347 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ASP B 349 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL B 306 " --> pdb=" O ASP B 349 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N HIS B 344 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE B 391 " --> pdb=" O HIS B 344 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE B 346 " --> pdb=" O ILE B 391 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N MET B 393 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N PHE B 348 " --> pdb=" O MET B 393 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL B 412 " --> pdb=" O GLY B 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 585 through 589 removed outlier: 3.784A pdb=" N PHE B 585 " --> pdb=" O LEU B 618 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG B 587 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL B 558 " --> pdb=" O ILE B 663 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N THR B 665 " --> pdb=" O VAL B 558 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU B 560 " --> pdb=" O THR B 665 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N THR B 667 " --> pdb=" O LEU B 560 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE B 562 " --> pdb=" O THR B 667 " (cutoff:3.500A) removed outlier: 9.499A pdb=" N ASN B 684 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N SER B 559 " --> pdb=" O ASN B 684 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N ILE B 686 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 561 " --> pdb=" O ILE B 686 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 304 through 307 removed outlier: 6.616A pdb=" N LYS C 304 " --> pdb=" O ILE C 347 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ASP C 349 " --> pdb=" O LYS C 304 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL C 306 " --> pdb=" O ASP C 349 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL C 412 " --> pdb=" O GLY C 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 585 through 589 removed outlier: 3.812A pdb=" N PHE C 585 " --> pdb=" O LEU C 618 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG C 587 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL C 558 " --> pdb=" O ILE C 663 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR C 665 " --> pdb=" O VAL C 558 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU C 560 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N THR C 667 " --> pdb=" O LEU C 560 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE C 562 " --> pdb=" O THR C 667 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN C 684 " --> pdb=" O SER C 559 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 304 through 307 removed outlier: 6.645A pdb=" N LYS D 304 " --> pdb=" O ILE D 347 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ASP D 349 " --> pdb=" O LYS D 304 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL D 306 " --> pdb=" O ASP D 349 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU D 277 " --> pdb=" O GLY D 392 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N THR D 394 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU D 279 " --> pdb=" O THR D 394 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N GLY D 276 " --> pdb=" O VAL D 412 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N VAL D 414 " --> pdb=" O GLY D 276 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU D 278 " --> pdb=" O VAL D 414 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 585 through 589 removed outlier: 3.849A pdb=" N PHE D 585 " --> pdb=" O LEU D 618 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG D 587 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN D 619 " --> pdb=" O ARG D 660 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL D 558 " --> pdb=" O ILE D 663 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N THR D 665 " --> pdb=" O VAL D 558 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU D 560 " --> pdb=" O THR D 665 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N THR D 667 " --> pdb=" O LEU D 560 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE D 562 " --> pdb=" O THR D 667 " (cutoff:3.500A) removed outlier: 9.428A pdb=" N ASN D 684 " --> pdb=" O LEU D 557 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N SER D 559 " --> pdb=" O ASN D 684 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N ILE D 686 " --> pdb=" O SER D 559 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU D 561 " --> pdb=" O ILE D 686 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 304 through 307 removed outlier: 6.788A pdb=" N LYS E 304 " --> pdb=" O ILE E 347 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ASP E 349 " --> pdb=" O LYS E 304 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL E 306 " --> pdb=" O ASP E 349 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET E 393 " --> pdb=" O PHE E 348 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU E 277 " --> pdb=" O GLY E 392 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N THR E 394 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU E 279 " --> pdb=" O THR E 394 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL E 412 " --> pdb=" O GLY E 276 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 585 through 589 removed outlier: 3.843A pdb=" N PHE E 585 " --> pdb=" O LEU E 618 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL E 558 " --> pdb=" O ILE E 663 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N THR E 665 " --> pdb=" O VAL E 558 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU E 560 " --> pdb=" O THR E 665 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N THR E 667 " --> pdb=" O LEU E 560 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE E 562 " --> pdb=" O THR E 667 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N ASN E 684 " --> pdb=" O LEU E 557 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N SER E 559 " --> pdb=" O ASN E 684 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N ILE E 686 " --> pdb=" O SER E 559 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU E 561 " --> pdb=" O ILE E 686 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 304 through 307 removed outlier: 6.493A pdb=" N HIS F 344 " --> pdb=" O LEU F 389 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE F 391 " --> pdb=" O HIS F 344 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE F 346 " --> pdb=" O ILE F 391 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N MET F 393 " --> pdb=" O ILE F 346 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N PHE F 348 " --> pdb=" O MET F 393 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL F 412 " --> pdb=" O GLY F 276 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 585 through 589 removed outlier: 3.749A pdb=" N PHE F 585 " --> pdb=" O LEU F 618 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG F 587 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN F 619 " --> pdb=" O ARG F 660 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL F 558 " --> pdb=" O ILE F 663 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N THR F 665 " --> pdb=" O VAL F 558 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU F 560 " --> pdb=" O THR F 665 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N THR F 667 " --> pdb=" O LEU F 560 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE F 562 " --> pdb=" O THR F 667 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN F 684 " --> pdb=" O SER F 559 " (cutoff:3.500A) 1000 hydrogen bonds defined for protein. 2871 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: 4.22 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5471 1.33 - 1.45: 4223 1.45 - 1.57: 14008 1.57 - 1.69: 48 1.69 - 1.81: 196 Bond restraints: 23946 Sorted by residual: bond pdb=" C4 ATP A 903 " pdb=" C5 ATP A 903 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.30e+01 bond pdb=" C4 ATP C 903 " pdb=" C5 ATP C 903 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.66e+01 bond pdb=" C4 ATP B 903 " pdb=" C5 ATP B 903 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.53e+01 bond pdb=" C4 ATP E 903 " pdb=" C5 ATP E 903 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.51e+01 bond pdb=" C4 ATP F 903 " pdb=" C5 ATP F 903 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.50e+01 ... (remaining 23941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.25: 32204 4.25 - 8.49: 145 8.49 - 12.74: 11 12.74 - 16.98: 5 16.98 - 21.23: 7 Bond angle restraints: 32372 Sorted by residual: angle pdb=" PB ATP B 903 " pdb=" O3B ATP B 903 " pdb=" PG ATP B 903 " ideal model delta sigma weight residual 139.87 118.64 21.23 1.00e+00 1.00e+00 4.51e+02 angle pdb=" PB ATP F 903 " pdb=" O3B ATP F 903 " pdb=" PG ATP F 903 " ideal model delta sigma weight residual 139.87 118.69 21.18 1.00e+00 1.00e+00 4.49e+02 angle pdb=" PB ATP E 903 " pdb=" O3B ATP E 903 " pdb=" PG ATP E 903 " ideal model delta sigma weight residual 139.87 120.03 19.84 1.00e+00 1.00e+00 3.93e+02 angle pdb=" PB ATP D 903 " pdb=" O3B ATP D 903 " pdb=" PG ATP D 903 " ideal model delta sigma weight residual 139.87 120.07 19.80 1.00e+00 1.00e+00 3.92e+02 angle pdb=" PB ATP C 903 " pdb=" O3B ATP C 903 " pdb=" PG ATP C 903 " ideal model delta sigma weight residual 139.87 120.44 19.43 1.00e+00 1.00e+00 3.78e+02 ... (remaining 32367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.22: 14522 30.22 - 60.45: 359 60.45 - 90.67: 44 90.67 - 120.90: 3 120.90 - 151.12: 3 Dihedral angle restraints: 14931 sinusoidal: 6304 harmonic: 8627 Sorted by residual: dihedral pdb=" O1B ADP D 902 " pdb=" O3A ADP D 902 " pdb=" PB ADP D 902 " pdb=" PA ADP D 902 " ideal model delta sinusoidal sigma weight residual -60.00 91.12 -151.12 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" O1B ADP C 902 " pdb=" O3A ADP C 902 " pdb=" PB ADP C 902 " pdb=" PA ADP C 902 " ideal model delta sinusoidal sigma weight residual -60.00 78.64 -138.64 1 2.00e+01 2.50e-03 4.20e+01 dihedral pdb=" O1B ADP B 902 " pdb=" O3A ADP B 902 " pdb=" PB ADP B 902 " pdb=" PA ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 78.55 -138.55 1 2.00e+01 2.50e-03 4.20e+01 ... (remaining 14928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 3553 0.096 - 0.192: 204 0.192 - 0.287: 2 0.287 - 0.383: 1 0.383 - 0.479: 5 Chirality restraints: 3765 Sorted by residual: chirality pdb=" CA PHE E 502 " pdb=" N PHE E 502 " pdb=" C PHE E 502 " pdb=" CB PHE E 502 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.73e+00 chirality pdb=" CA PHE A 502 " pdb=" N PHE A 502 " pdb=" C PHE A 502 " pdb=" CB PHE A 502 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CA PHE C 502 " pdb=" N PHE C 502 " pdb=" C PHE C 502 " pdb=" CB PHE C 502 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.26e+00 ... (remaining 3762 not shown) Planarity restraints: 4141 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 436 " -0.187 9.50e-02 1.11e+02 9.44e-02 2.74e+01 pdb=" NE ARG E 436 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG E 436 " 0.085 2.00e-02 2.50e+03 pdb=" NH1 ARG E 436 " -0.025 2.00e-02 2.50e+03 pdb=" NH2 ARG E 436 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 335 " -0.113 9.50e-02 1.11e+02 6.48e-02 2.23e+01 pdb=" NE ARG B 335 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG B 335 " 0.080 2.00e-02 2.50e+03 pdb=" NH1 ARG B 335 " -0.025 2.00e-02 2.50e+03 pdb=" NH2 ARG B 335 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 544 " -0.120 9.50e-02 1.11e+02 6.68e-02 2.13e+01 pdb=" NE ARG D 544 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG D 544 " 0.078 2.00e-02 2.50e+03 pdb=" NH1 ARG D 544 " -0.024 2.00e-02 2.50e+03 pdb=" NH2 ARG D 544 " -0.030 2.00e-02 2.50e+03 ... (remaining 4138 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 76 2.51 - 3.11: 17696 3.11 - 3.71: 31398 3.71 - 4.30: 44854 4.30 - 4.90: 75462 Nonbonded interactions: 169486 Sorted by model distance: nonbonded pdb="MG MG F 901 " pdb=" O1G ATP F 903 " model vdw 1.914 2.170 nonbonded pdb="MG MG E 901 " pdb=" O1G ATP E 903 " model vdw 1.916 2.170 nonbonded pdb="MG MG A 901 " pdb=" O3G ATP A 903 " model vdw 1.968 2.170 nonbonded pdb=" OG1 THR A 571 " pdb="MG MG A 901 " model vdw 1.968 2.170 nonbonded pdb=" OG1 THR D 571 " pdb="MG MG D 901 " model vdw 2.000 2.170 ... (remaining 169481 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 246 through 294 or resid 303 through 336 or resid 342 thro \ ugh 903)) selection = (chain 'B' and (resid 246 through 294 or resid 303 through 336 or resid 342 thro \ ugh 479 or resid 493 through 903)) selection = (chain 'C' and (resid 246 through 294 or resid 303 through 336 or resid 342 thro \ ugh 479 or resid 493 through 903)) selection = (chain 'D' and (resid 246 through 294 or resid 303 through 336 or resid 342 thro \ ugh 479 or resid 493 through 903)) selection = (chain 'E' and (resid 246 through 294 or resid 303 through 336 or resid 342 thro \ ugh 479 or resid 493 through 903)) selection = (chain 'F' and (resid 246 through 479 or resid 493 through 903)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.280 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 23946 Z= 0.297 Angle : 0.940 21.230 32372 Z= 0.639 Chirality : 0.049 0.479 3765 Planarity : 0.007 0.094 4141 Dihedral : 13.553 151.122 9319 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.92 % Favored : 96.95 % Rotamer: Outliers : 0.08 % Allowed : 0.57 % Favored : 99.35 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.14), residues: 2947 helix: -1.76 (0.11), residues: 1359 sheet: 0.92 (0.23), residues: 398 loop : -0.50 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.083 0.010 ARG E 436 TYR 0.026 0.004 TYR B 670 PHE 0.018 0.002 PHE E 726 TRP 0.008 0.003 TRP C 632 HIS 0.010 0.003 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00453 (23946) covalent geometry : angle 0.93990 (32372) hydrogen bonds : bond 0.27811 ( 1000) hydrogen bonds : angle 7.83217 ( 2871) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 174 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 686 ILE cc_start: 0.6607 (mt) cc_final: 0.6327 (mt) REVERT: B 299 ASN cc_start: 0.7602 (t0) cc_final: 0.7344 (t0) REVERT: B 440 MET cc_start: 0.7421 (mtt) cc_final: 0.6969 (mtt) REVERT: B 748 ASN cc_start: 0.8473 (t0) cc_final: 0.8012 (t0) REVERT: D 324 ARG cc_start: 0.9000 (ttp80) cc_final: 0.8782 (tmm-80) REVERT: F 454 THR cc_start: 0.7420 (p) cc_final: 0.6996 (p) outliers start: 2 outliers final: 0 residues processed: 176 average time/residue: 0.1572 time to fit residues: 44.0063 Evaluate side-chains 127 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 641 ASN B 674 GLN C 641 ASN C 657 GLN E 370 ASN F 725 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.127340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.083210 restraints weight = 43429.531| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.26 r_work: 0.2959 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23946 Z= 0.145 Angle : 0.620 7.489 32372 Z= 0.328 Chirality : 0.044 0.179 3765 Planarity : 0.004 0.052 4141 Dihedral : 10.180 139.008 3447 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.34 % Allowed : 3.64 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.15), residues: 2947 helix: -0.32 (0.13), residues: 1472 sheet: 1.07 (0.22), residues: 416 loop : -0.26 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 544 TYR 0.015 0.001 TYR F 670 PHE 0.016 0.001 PHE F 252 TRP 0.007 0.001 TRP D 632 HIS 0.005 0.001 HIS B 344 Details of bonding type rmsd covalent geometry : bond 0.00279 (23946) covalent geometry : angle 0.61965 (32372) hydrogen bonds : bond 0.05621 ( 1000) hydrogen bonds : angle 5.02497 ( 2871) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: A 440 MET cc_start: 0.7218 (mmt) cc_final: 0.6985 (mmt) REVERT: A 686 ILE cc_start: 0.6671 (mt) cc_final: 0.6431 (mm) REVERT: B 299 ASN cc_start: 0.8078 (t0) cc_final: 0.7800 (t0) REVERT: B 324 ARG cc_start: 0.8172 (mtm-85) cc_final: 0.7865 (mpp80) REVERT: B 748 ASN cc_start: 0.8294 (t0) cc_final: 0.7970 (t0) REVERT: D 646 MET cc_start: 0.8712 (tpp) cc_final: 0.8452 (tpt) REVERT: F 305 ILE cc_start: 0.6636 (tt) cc_final: 0.6200 (mp) REVERT: F 441 MET cc_start: 0.7734 (mtp) cc_final: 0.7379 (mtp) outliers start: 9 outliers final: 4 residues processed: 163 average time/residue: 0.1599 time to fit residues: 40.6170 Evaluate side-chains 136 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain F residue 433 LYS Chi-restraints excluded: chain F residue 719 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 270 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 82 optimal weight: 0.0980 chunk 180 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 GLN ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 ASN F 536 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.124584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.079245 restraints weight = 43829.929| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.10 r_work: 0.2897 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 23946 Z= 0.224 Angle : 0.678 9.950 32372 Z= 0.350 Chirality : 0.046 0.207 3765 Planarity : 0.005 0.053 4141 Dihedral : 9.960 123.804 3447 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.77 % Allowed : 6.13 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.15), residues: 2947 helix: -0.07 (0.13), residues: 1480 sheet: 0.86 (0.23), residues: 406 loop : -0.51 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 712 TYR 0.018 0.002 TYR C 670 PHE 0.020 0.002 PHE D 585 TRP 0.011 0.002 TRP D 632 HIS 0.005 0.002 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00561 (23946) covalent geometry : angle 0.67803 (32372) hydrogen bonds : bond 0.06850 ( 1000) hydrogen bonds : angle 4.85467 ( 2871) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 738 GLU cc_start: 0.6182 (OUTLIER) cc_final: 0.5831 (tm-30) REVERT: B 324 ARG cc_start: 0.8228 (mtm-85) cc_final: 0.7924 (mpp80) REVERT: C 328 LYS cc_start: 0.8773 (tttp) cc_final: 0.8328 (mmmm) REVERT: C 723 CYS cc_start: 0.7550 (t) cc_final: 0.6991 (t) REVERT: D 285 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8636 (p) REVERT: F 305 ILE cc_start: 0.6821 (tt) cc_final: 0.6380 (mp) REVERT: F 327 PHE cc_start: 0.2694 (OUTLIER) cc_final: 0.1985 (t80) REVERT: F 441 MET cc_start: 0.7680 (mtp) cc_final: 0.7360 (mtp) outliers start: 20 outliers final: 5 residues processed: 156 average time/residue: 0.1451 time to fit residues: 37.2318 Evaluate side-chains 136 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 518 GLU Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 719 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 286 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 274 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 236 optimal weight: 0.9990 chunk 173 optimal weight: 0.2980 chunk 216 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.125683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.081141 restraints weight = 43343.542| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.23 r_work: 0.2941 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23946 Z= 0.116 Angle : 0.545 9.235 32372 Z= 0.279 Chirality : 0.041 0.191 3765 Planarity : 0.004 0.055 4141 Dihedral : 9.231 125.307 3447 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.84 % Allowed : 7.09 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 2947 helix: 0.45 (0.14), residues: 1437 sheet: 0.81 (0.22), residues: 421 loop : -0.30 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 324 TYR 0.011 0.001 TYR F 280 PHE 0.011 0.001 PHE E 248 TRP 0.006 0.001 TRP B 632 HIS 0.002 0.001 HIS A 742 Details of bonding type rmsd covalent geometry : bond 0.00254 (23946) covalent geometry : angle 0.54525 (32372) hydrogen bonds : bond 0.04330 ( 1000) hydrogen bonds : angle 4.39544 ( 2871) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 350 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7823 (mt-10) REVERT: A 676 MET cc_start: 0.7556 (mtt) cc_final: 0.7355 (mtm) REVERT: B 324 ARG cc_start: 0.8231 (mtm-85) cc_final: 0.7859 (mpp80) REVERT: B 701 MET cc_start: 0.8517 (mtm) cc_final: 0.8313 (mtm) REVERT: C 324 ARG cc_start: 0.8104 (tpt170) cc_final: 0.7634 (tpt90) REVERT: C 328 LYS cc_start: 0.8642 (tttp) cc_final: 0.7660 (mttp) REVERT: C 723 CYS cc_start: 0.7500 (t) cc_final: 0.6914 (t) REVERT: D 345 ILE cc_start: 0.8552 (tt) cc_final: 0.8300 (mt) REVERT: F 305 ILE cc_start: 0.6791 (tt) cc_final: 0.6376 (mp) outliers start: 22 outliers final: 10 residues processed: 159 average time/residue: 0.1554 time to fit residues: 40.1765 Evaluate side-chains 141 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 518 GLU Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 707 LEU Chi-restraints excluded: chain F residue 719 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 235 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 233 optimal weight: 4.9990 chunk 258 optimal weight: 2.9990 chunk 259 optimal weight: 6.9990 chunk 281 optimal weight: 0.3980 chunk 293 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 291 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN F 684 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.125577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.081024 restraints weight = 43123.081| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.18 r_work: 0.2936 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23946 Z= 0.120 Angle : 0.538 8.056 32372 Z= 0.271 Chirality : 0.041 0.195 3765 Planarity : 0.004 0.054 4141 Dihedral : 8.800 117.399 3447 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.00 % Allowed : 7.82 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.16), residues: 2947 helix: 0.71 (0.14), residues: 1450 sheet: 0.91 (0.23), residues: 421 loop : -0.26 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 335 TYR 0.011 0.001 TYR F 280 PHE 0.012 0.001 PHE C 457 TRP 0.005 0.001 TRP B 632 HIS 0.002 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00274 (23946) covalent geometry : angle 0.53800 (32372) hydrogen bonds : bond 0.04259 ( 1000) hydrogen bonds : angle 4.19582 ( 2871) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: A 350 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7857 (mt-10) REVERT: B 335 ARG cc_start: 0.8507 (mmm-85) cc_final: 0.8033 (mmt-90) REVERT: B 701 MET cc_start: 0.8515 (mtm) cc_final: 0.8197 (mtp) REVERT: C 324 ARG cc_start: 0.8150 (tpt170) cc_final: 0.7886 (tpt90) REVERT: C 328 LYS cc_start: 0.8659 (tttp) cc_final: 0.7682 (mttp) REVERT: C 374 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8283 (mp10) REVERT: C 723 CYS cc_start: 0.7558 (t) cc_final: 0.6972 (t) REVERT: D 285 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8441 (p) REVERT: D 345 ILE cc_start: 0.8580 (tt) cc_final: 0.8369 (mt) REVERT: F 305 ILE cc_start: 0.6884 (tt) cc_final: 0.6472 (mp) REVERT: F 327 PHE cc_start: 0.2391 (OUTLIER) cc_final: 0.2120 (t80) REVERT: F 707 LEU cc_start: 0.6708 (OUTLIER) cc_final: 0.6469 (pp) outliers start: 26 outliers final: 11 residues processed: 158 average time/residue: 0.1626 time to fit residues: 41.3107 Evaluate side-chains 144 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 518 GLU Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 707 LEU Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 719 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 272 optimal weight: 5.9990 chunk 138 optimal weight: 0.0570 chunk 285 optimal weight: 0.3980 chunk 143 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 213 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 153 optimal weight: 0.8980 chunk 204 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.128792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.083669 restraints weight = 43310.041| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.12 r_work: 0.2990 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23946 Z= 0.093 Angle : 0.498 8.456 32372 Z= 0.249 Chirality : 0.040 0.186 3765 Planarity : 0.004 0.057 4141 Dihedral : 8.399 115.872 3447 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.11 % Allowed : 8.36 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.16), residues: 2947 helix: 0.93 (0.14), residues: 1478 sheet: 1.14 (0.23), residues: 420 loop : -0.14 (0.20), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 324 TYR 0.009 0.001 TYR F 670 PHE 0.008 0.001 PHE E 248 TRP 0.003 0.001 TRP B 632 HIS 0.001 0.000 HIS D 344 Details of bonding type rmsd covalent geometry : bond 0.00194 (23946) covalent geometry : angle 0.49759 (32372) hydrogen bonds : bond 0.03204 ( 1000) hydrogen bonds : angle 4.01980 ( 2871) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: A 350 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7858 (mt-10) REVERT: A 686 ILE cc_start: 0.6745 (mt) cc_final: 0.6187 (mm) REVERT: B 701 MET cc_start: 0.8535 (mtm) cc_final: 0.8174 (mtp) REVERT: C 374 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8273 (mp10) REVERT: C 723 CYS cc_start: 0.7526 (t) cc_final: 0.6909 (t) REVERT: D 285 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8387 (p) REVERT: F 266 ILE cc_start: 0.7323 (OUTLIER) cc_final: 0.6909 (mt) REVERT: F 305 ILE cc_start: 0.7036 (tt) cc_final: 0.6632 (mp) REVERT: F 707 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6505 (pp) outliers start: 29 outliers final: 8 residues processed: 167 average time/residue: 0.1549 time to fit residues: 42.0112 Evaluate side-chains 140 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 719 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 148 optimal weight: 0.9980 chunk 114 optimal weight: 0.4980 chunk 36 optimal weight: 6.9990 chunk 260 optimal weight: 7.9990 chunk 287 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 266 optimal weight: 10.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.125927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.080503 restraints weight = 43408.463| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.10 r_work: 0.2933 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23946 Z= 0.147 Angle : 0.555 8.193 32372 Z= 0.278 Chirality : 0.042 0.200 3765 Planarity : 0.004 0.054 4141 Dihedral : 8.593 110.779 3447 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.26 % Allowed : 8.55 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.16), residues: 2947 helix: 0.87 (0.14), residues: 1473 sheet: 1.02 (0.24), residues: 419 loop : -0.21 (0.20), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 335 TYR 0.011 0.001 TYR F 280 PHE 0.015 0.001 PHE C 457 TRP 0.007 0.001 TRP E 632 HIS 0.003 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00360 (23946) covalent geometry : angle 0.55528 (32372) hydrogen bonds : bond 0.04524 ( 1000) hydrogen bonds : angle 4.13991 ( 2871) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 1.087 Fit side-chains revert: symmetry clash REVERT: A 350 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7833 (mt-10) REVERT: A 435 MET cc_start: 0.7096 (ttp) cc_final: 0.6857 (ttm) REVERT: A 626 LEU cc_start: 0.6250 (OUTLIER) cc_final: 0.5960 (tt) REVERT: B 324 ARG cc_start: 0.8517 (mtm180) cc_final: 0.8150 (mpp80) REVERT: B 335 ARG cc_start: 0.8560 (mmm-85) cc_final: 0.8041 (mmt-90) REVERT: B 461 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7844 (mt-10) REVERT: B 701 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8333 (mtm) REVERT: C 324 ARG cc_start: 0.8387 (tpt170) cc_final: 0.7734 (tpt90) REVERT: C 328 LYS cc_start: 0.8785 (tttp) cc_final: 0.7741 (mttp) REVERT: C 374 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8274 (mp10) REVERT: C 393 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8552 (mtp) REVERT: C 723 CYS cc_start: 0.7544 (t) cc_final: 0.6918 (t) REVERT: D 285 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8538 (p) REVERT: F 266 ILE cc_start: 0.7340 (OUTLIER) cc_final: 0.6923 (mt) REVERT: F 305 ILE cc_start: 0.7010 (tt) cc_final: 0.6580 (mp) REVERT: F 327 PHE cc_start: 0.2251 (OUTLIER) cc_final: 0.1348 (t80) REVERT: F 707 LEU cc_start: 0.6835 (OUTLIER) cc_final: 0.6595 (pp) outliers start: 33 outliers final: 13 residues processed: 157 average time/residue: 0.1523 time to fit residues: 39.2174 Evaluate side-chains 146 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 707 LEU Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 707 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 166 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 233 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 208 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.126465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.081118 restraints weight = 43301.516| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.12 r_work: 0.2946 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23946 Z= 0.120 Angle : 0.525 8.877 32372 Z= 0.262 Chirality : 0.041 0.195 3765 Planarity : 0.004 0.055 4141 Dihedral : 8.527 110.340 3447 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.80 % Allowed : 9.12 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.16), residues: 2947 helix: 0.93 (0.14), residues: 1477 sheet: 0.97 (0.24), residues: 420 loop : -0.24 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 324 TYR 0.009 0.001 TYR F 280 PHE 0.010 0.001 PHE D 585 TRP 0.006 0.001 TRP B 632 HIS 0.002 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00281 (23946) covalent geometry : angle 0.52481 (32372) hydrogen bonds : bond 0.03989 ( 1000) hydrogen bonds : angle 4.06644 ( 2871) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 350 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7832 (mt-10) REVERT: B 324 ARG cc_start: 0.8512 (mtm180) cc_final: 0.8130 (mpp80) REVERT: B 335 ARG cc_start: 0.8537 (mmm-85) cc_final: 0.8019 (mmt-90) REVERT: B 461 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7812 (mt-10) REVERT: C 328 LYS cc_start: 0.8765 (tttp) cc_final: 0.8516 (mttp) REVERT: C 374 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8267 (mp10) REVERT: C 393 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8500 (mtp) REVERT: C 723 CYS cc_start: 0.7555 (t) cc_final: 0.6943 (t) REVERT: D 285 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8536 (p) REVERT: F 266 ILE cc_start: 0.7257 (OUTLIER) cc_final: 0.6852 (mt) REVERT: F 305 ILE cc_start: 0.7061 (tt) cc_final: 0.6630 (mp) REVERT: F 707 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6580 (pp) outliers start: 21 outliers final: 11 residues processed: 142 average time/residue: 0.1566 time to fit residues: 36.2613 Evaluate side-chains 142 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 707 LEU Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 707 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 19 optimal weight: 30.0000 chunk 167 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 296 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 278 optimal weight: 7.9990 chunk 189 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 344 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.126311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.080916 restraints weight = 43488.057| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.11 r_work: 0.2939 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23946 Z= 0.126 Angle : 0.532 9.052 32372 Z= 0.265 Chirality : 0.041 0.198 3765 Planarity : 0.004 0.055 4141 Dihedral : 8.405 106.337 3447 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.88 % Allowed : 9.20 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.16), residues: 2947 helix: 0.95 (0.14), residues: 1477 sheet: 0.89 (0.24), residues: 420 loop : -0.27 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 324 TYR 0.013 0.001 TYR C 334 PHE 0.012 0.001 PHE D 585 TRP 0.005 0.001 TRP B 632 HIS 0.002 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00300 (23946) covalent geometry : angle 0.53211 (32372) hydrogen bonds : bond 0.04097 ( 1000) hydrogen bonds : angle 4.04001 ( 2871) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 350 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7870 (mt-10) REVERT: B 324 ARG cc_start: 0.8519 (mtm180) cc_final: 0.8129 (mpp80) REVERT: B 335 ARG cc_start: 0.8549 (mmm-85) cc_final: 0.8029 (mmt-90) REVERT: B 461 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7861 (mt-10) REVERT: C 324 ARG cc_start: 0.8351 (tpt170) cc_final: 0.7726 (tpt90) REVERT: C 328 LYS cc_start: 0.8802 (tttp) cc_final: 0.7883 (mttp) REVERT: C 374 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8264 (mp10) REVERT: C 393 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8539 (mtp) REVERT: C 723 CYS cc_start: 0.7579 (t) cc_final: 0.6963 (t) REVERT: D 285 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8579 (p) REVERT: F 266 ILE cc_start: 0.7259 (OUTLIER) cc_final: 0.6851 (mt) REVERT: F 305 ILE cc_start: 0.7070 (tt) cc_final: 0.6684 (mp) REVERT: F 707 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6621 (pp) outliers start: 23 outliers final: 14 residues processed: 149 average time/residue: 0.1521 time to fit residues: 37.3475 Evaluate side-chains 148 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 707 LEU Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 510 THR Chi-restraints excluded: chain F residue 707 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 107 optimal weight: 6.9990 chunk 195 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 175 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 243 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.126144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.080958 restraints weight = 43536.937| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.11 r_work: 0.2928 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23946 Z= 0.140 Angle : 0.543 9.294 32372 Z= 0.271 Chirality : 0.042 0.202 3765 Planarity : 0.004 0.055 4141 Dihedral : 8.436 103.457 3447 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.92 % Allowed : 9.31 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.16), residues: 2947 helix: 0.90 (0.14), residues: 1476 sheet: 0.82 (0.24), residues: 421 loop : -0.29 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 324 TYR 0.010 0.001 TYR C 334 PHE 0.013 0.001 PHE D 585 TRP 0.007 0.001 TRP E 632 HIS 0.003 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00339 (23946) covalent geometry : angle 0.54305 (32372) hydrogen bonds : bond 0.04353 ( 1000) hydrogen bonds : angle 4.08056 ( 2871) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 350 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7875 (mt-10) REVERT: B 324 ARG cc_start: 0.8520 (mtm180) cc_final: 0.8129 (mpp80) REVERT: B 335 ARG cc_start: 0.8577 (mmm-85) cc_final: 0.8056 (mmt-90) REVERT: B 461 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: C 324 ARG cc_start: 0.8274 (tpt170) cc_final: 0.7667 (tpt90) REVERT: C 328 LYS cc_start: 0.8727 (tttp) cc_final: 0.7901 (mttp) REVERT: C 374 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8247 (mp10) REVERT: C 393 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8584 (mtp) REVERT: C 723 CYS cc_start: 0.7599 (t) cc_final: 0.6981 (t) REVERT: D 285 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8614 (p) REVERT: F 266 ILE cc_start: 0.7175 (OUTLIER) cc_final: 0.6778 (mt) REVERT: F 305 ILE cc_start: 0.7106 (tt) cc_final: 0.6713 (mp) REVERT: F 707 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6642 (pp) outliers start: 24 outliers final: 16 residues processed: 149 average time/residue: 0.1549 time to fit residues: 37.9088 Evaluate side-chains 150 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 707 LEU Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 510 THR Chi-restraints excluded: chain F residue 707 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 184 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 153 optimal weight: 0.3980 chunk 158 optimal weight: 5.9990 chunk 216 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 100 optimal weight: 0.4980 chunk 55 optimal weight: 8.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 748 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.125942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.080613 restraints weight = 43307.030| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.10 r_work: 0.2934 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23946 Z= 0.129 Angle : 0.534 9.287 32372 Z= 0.267 Chirality : 0.041 0.199 3765 Planarity : 0.004 0.055 4141 Dihedral : 8.273 101.019 3447 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.00 % Allowed : 9.51 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.16), residues: 2947 helix: 0.95 (0.14), residues: 1476 sheet: 0.83 (0.24), residues: 420 loop : -0.31 (0.20), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 335 TYR 0.010 0.001 TYR C 334 PHE 0.011 0.001 PHE D 585 TRP 0.006 0.001 TRP E 632 HIS 0.002 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00307 (23946) covalent geometry : angle 0.53438 (32372) hydrogen bonds : bond 0.04110 ( 1000) hydrogen bonds : angle 4.02951 ( 2871) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5431.89 seconds wall clock time: 93 minutes 40.39 seconds (5620.39 seconds total)