Starting phenix.real_space_refine on Fri Jun 27 14:12:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ip0_60751/06_2025/9ip0_60751.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ip0_60751/06_2025/9ip0_60751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ip0_60751/06_2025/9ip0_60751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ip0_60751/06_2025/9ip0_60751.map" model { file = "/net/cci-nas-00/data/ceres_data/9ip0_60751/06_2025/9ip0_60751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ip0_60751/06_2025/9ip0_60751.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 28 5.49 5 S 98 5.16 5 C 20013 2.51 5 N 5866 2.21 5 O 6048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32053 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4525 Classifications: {'peptide': 574} Link IDs: {'PTRANS': 21, 'TRANS': 552} Chain breaks: 5 Chain: "B" Number of atoms: 4525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4525 Classifications: {'peptide': 574} Link IDs: {'PTRANS': 21, 'TRANS': 552} Chain breaks: 5 Chain: "C" Number of atoms: 4525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4525 Classifications: {'peptide': 574} Link IDs: {'PTRANS': 21, 'TRANS': 552} Chain breaks: 5 Chain: "D" Number of atoms: 4525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4525 Classifications: {'peptide': 574} Link IDs: {'PTRANS': 21, 'TRANS': 552} Chain breaks: 5 Chain: "E" Number of atoms: 4525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4525 Classifications: {'peptide': 574} Link IDs: {'PTRANS': 21, 'TRANS': 552} Chain breaks: 5 Chain: "F" Number of atoms: 4525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4525 Classifications: {'peptide': 574} Link IDs: {'PTRANS': 21, 'TRANS': 552} Chain breaks: 5 Chain: "G" Number of atoms: 4525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4525 Classifications: {'peptide': 574} Link IDs: {'PTRANS': 21, 'TRANS': 552} Chain breaks: 5 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.12, per 1000 atoms: 0.53 Number of scatterers: 32053 At special positions: 0 Unit cell: (166.1, 169.4, 104.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 98 16.00 P 28 15.00 O 6048 8.00 N 5866 7.00 C 20013 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: 6.79 Conformation dependent library (CDL) restraints added in 3.6 seconds 7868 Ramachandran restraints generated. 3934 Oldfield, 0 Emsley, 3934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7476 Finding SS restraints... Secondary structure from input PDB file: 217 helices and 30 sheets defined 59.2% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.51 Creating SS restraints... Processing helix chain 'A' and resid 174 through 180 removed outlier: 3.545A pdb=" N ALA A 177 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY A 178 " --> pdb=" O GLU A 175 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 180 " --> pdb=" O ALA A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 198 removed outlier: 3.938A pdb=" N ILE A 190 " --> pdb=" O ARG A 186 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 229 Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 255 through 269 Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.847A pdb=" N VAL A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 309 Proline residue: A 304 - end of helix Processing helix chain 'A' and resid 318 through 325 Processing helix chain 'A' and resid 326 through 329 removed outlier: 3.613A pdb=" N ASP A 329 " --> pdb=" O VAL A 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 326 through 329' Processing helix chain 'A' and resid 331 through 335 removed outlier: 3.510A pdb=" N ARG A 335 " --> pdb=" O PHE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 365 removed outlier: 3.619A pdb=" N THR A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER A 351 " --> pdb=" O PRO A 347 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LYS A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 380 removed outlier: 3.768A pdb=" N LEU A 373 " --> pdb=" O GLN A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 392 through 409 removed outlier: 3.691A pdb=" N LEU A 396 " --> pdb=" O LYS A 392 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG A 405 " --> pdb=" O CYS A 401 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 429 Processing helix chain 'A' and resid 536 through 547 removed outlier: 3.583A pdb=" N GLU A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 541 " --> pdb=" O GLN A 537 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL A 542 " --> pdb=" O ILE A 538 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR A 546 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 568 removed outlier: 4.772A pdb=" N ALA A 565 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASP A 566 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 592 removed outlier: 3.838A pdb=" N GLY A 592 " --> pdb=" O ARG A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 625 removed outlier: 3.531A pdb=" N LEU A 616 " --> pdb=" O GLY A 612 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA A 617 " --> pdb=" O LYS A 613 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE A 625 " --> pdb=" O ALA A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 643 No H-bonds generated for 'chain 'A' and resid 641 through 643' Processing helix chain 'A' and resid 644 through 649 Processing helix chain 'A' and resid 680 through 684 Processing helix chain 'A' and resid 685 through 690 Processing helix chain 'A' and resid 692 through 699 removed outlier: 3.595A pdb=" N LEU A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 730 removed outlier: 3.677A pdb=" N GLY A 730 " --> pdb=" O HIS A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 752 Processing helix chain 'A' and resid 755 through 759 Processing helix chain 'A' and resid 770 through 791 removed outlier: 3.729A pdb=" N ASP A 784 " --> pdb=" O LEU A 780 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL A 785 " --> pdb=" O GLN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 810 removed outlier: 3.597A pdb=" N LEU A 803 " --> pdb=" O THR A 799 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 805 " --> pdb=" O ALA A 801 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER A 810 " --> pdb=" O ILE A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 838 removed outlier: 3.681A pdb=" N ARG A 821 " --> pdb=" O ALA A 817 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N THR A 830 " --> pdb=" O LYS A 826 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN A 838 " --> pdb=" O LYS A 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 179 removed outlier: 3.661A pdb=" N GLY B 178 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 198 removed outlier: 3.951A pdb=" N ILE B 190 " --> pdb=" O ARG B 186 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 229 Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 244 through 249 Processing helix chain 'B' and resid 255 through 269 Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 282 through 288 removed outlier: 3.818A pdb=" N VAL B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 309 Proline residue: B 304 - end of helix Processing helix chain 'B' and resid 318 through 325 removed outlier: 3.556A pdb=" N TYR B 322 " --> pdb=" O THR B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 335 removed outlier: 3.511A pdb=" N ARG B 335 " --> pdb=" O PHE B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 365 removed outlier: 3.574A pdb=" N THR B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 350 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER B 351 " --> pdb=" O PRO B 347 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU B 358 " --> pdb=" O ARG B 354 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N LYS B 359 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 380 Processing helix chain 'B' and resid 389 through 391 No H-bonds generated for 'chain 'B' and resid 389 through 391' Processing helix chain 'B' and resid 392 through 409 removed outlier: 3.678A pdb=" N LEU B 396 " --> pdb=" O LYS B 392 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG B 405 " --> pdb=" O CYS B 401 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 429 Processing helix chain 'B' and resid 536 through 547 removed outlier: 3.707A pdb=" N GLU B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL B 541 " --> pdb=" O GLN B 537 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 542 " --> pdb=" O ILE B 538 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR B 546 " --> pdb=" O VAL B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 569 removed outlier: 4.899A pdb=" N ALA B 565 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ASP B 566 " --> pdb=" O VAL B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 592 removed outlier: 3.801A pdb=" N GLY B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 625 removed outlier: 3.531A pdb=" N LEU B 616 " --> pdb=" O GLY B 612 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA B 617 " --> pdb=" O LYS B 613 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 625 " --> pdb=" O ALA B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 643 No H-bonds generated for 'chain 'B' and resid 641 through 643' Processing helix chain 'B' and resid 644 through 649 Processing helix chain 'B' and resid 680 through 684 Processing helix chain 'B' and resid 685 through 690 Processing helix chain 'B' and resid 692 through 699 removed outlier: 3.593A pdb=" N LEU B 696 " --> pdb=" O LEU B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 730 removed outlier: 3.948A pdb=" N GLY B 730 " --> pdb=" O HIS B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 752 Processing helix chain 'B' and resid 755 through 759 Processing helix chain 'B' and resid 770 through 791 removed outlier: 3.738A pdb=" N ASP B 784 " --> pdb=" O LEU B 780 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL B 785 " --> pdb=" O GLN B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 810 removed outlier: 3.554A pdb=" N LEU B 803 " --> pdb=" O THR B 799 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER B 810 " --> pdb=" O ILE B 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 838 removed outlier: 3.696A pdb=" N ARG B 821 " --> pdb=" O ALA B 817 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR B 830 " --> pdb=" O LYS B 826 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN B 838 " --> pdb=" O LYS B 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 179 removed outlier: 3.664A pdb=" N ALA C 177 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY C 178 " --> pdb=" O GLU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 198 removed outlier: 3.943A pdb=" N ILE C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER C 198 " --> pdb=" O VAL C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 229 Processing helix chain 'C' and resid 232 through 236 Processing helix chain 'C' and resid 244 through 249 Processing helix chain 'C' and resid 255 through 269 Processing helix chain 'C' and resid 282 through 288 removed outlier: 3.721A pdb=" N VAL C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 309 Proline residue: C 304 - end of helix Processing helix chain 'C' and resid 318 through 325 Processing helix chain 'C' and resid 326 through 329 removed outlier: 3.683A pdb=" N ASP C 329 " --> pdb=" O VAL C 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 326 through 329' Processing helix chain 'C' and resid 331 through 335 removed outlier: 3.544A pdb=" N ARG C 335 " --> pdb=" O PHE C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 365 removed outlier: 3.547A pdb=" N THR C 349 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE C 350 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER C 351 " --> pdb=" O PRO C 347 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLU C 358 " --> pdb=" O ARG C 354 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LYS C 359 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 380 Processing helix chain 'C' and resid 389 through 391 No H-bonds generated for 'chain 'C' and resid 389 through 391' Processing helix chain 'C' and resid 392 through 409 removed outlier: 3.711A pdb=" N LEU C 396 " --> pdb=" O LYS C 392 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA C 400 " --> pdb=" O LEU C 396 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG C 405 " --> pdb=" O CYS C 401 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 406 " --> pdb=" O ALA C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 429 Processing helix chain 'C' and resid 536 through 547 removed outlier: 3.535A pdb=" N GLU C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL C 541 " --> pdb=" O GLN C 537 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL C 542 " --> pdb=" O ILE C 538 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR C 546 " --> pdb=" O VAL C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 569 removed outlier: 4.901A pdb=" N ALA C 565 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASP C 566 " --> pdb=" O VAL C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 592 removed outlier: 3.791A pdb=" N GLY C 592 " --> pdb=" O ARG C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 625 removed outlier: 3.536A pdb=" N LEU C 616 " --> pdb=" O GLY C 612 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA C 617 " --> pdb=" O LYS C 613 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE C 625 " --> pdb=" O ALA C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 643 No H-bonds generated for 'chain 'C' and resid 641 through 643' Processing helix chain 'C' and resid 644 through 649 Processing helix chain 'C' and resid 680 through 684 Processing helix chain 'C' and resid 685 through 690 Processing helix chain 'C' and resid 692 through 699 Processing helix chain 'C' and resid 723 through 730 removed outlier: 4.177A pdb=" N GLY C 730 " --> pdb=" O HIS C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 752 Processing helix chain 'C' and resid 755 through 759 Processing helix chain 'C' and resid 770 through 791 removed outlier: 3.649A pdb=" N ASP C 784 " --> pdb=" O LEU C 780 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL C 785 " --> pdb=" O GLN C 781 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 810 removed outlier: 3.727A pdb=" N SER C 810 " --> pdb=" O ILE C 806 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 838 removed outlier: 3.635A pdb=" N ARG C 821 " --> pdb=" O ALA C 817 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR C 830 " --> pdb=" O LYS C 826 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN C 838 " --> pdb=" O LYS C 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 179 removed outlier: 3.589A pdb=" N ALA D 177 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY D 178 " --> pdb=" O GLU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 198 removed outlier: 3.939A pdb=" N ILE D 190 " --> pdb=" O ARG D 186 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER D 198 " --> pdb=" O VAL D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 229 Processing helix chain 'D' and resid 232 through 236 Processing helix chain 'D' and resid 244 through 249 Processing helix chain 'D' and resid 255 through 269 Processing helix chain 'D' and resid 270 through 272 No H-bonds generated for 'chain 'D' and resid 270 through 272' Processing helix chain 'D' and resid 282 through 288 removed outlier: 3.810A pdb=" N VAL D 286 " --> pdb=" O GLU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 309 Proline residue: D 304 - end of helix Processing helix chain 'D' and resid 318 through 325 removed outlier: 3.520A pdb=" N TYR D 322 " --> pdb=" O THR D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 335 Processing helix chain 'D' and resid 345 through 365 removed outlier: 3.587A pdb=" N THR D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE D 350 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER D 351 " --> pdb=" O PRO D 347 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLU D 358 " --> pdb=" O ARG D 354 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LYS D 359 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR D 360 " --> pdb=" O LEU D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 380 removed outlier: 3.781A pdb=" N LEU D 373 " --> pdb=" O GLN D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 391 No H-bonds generated for 'chain 'D' and resid 389 through 391' Processing helix chain 'D' and resid 392 through 409 removed outlier: 3.690A pdb=" N LEU D 396 " --> pdb=" O LYS D 392 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA D 400 " --> pdb=" O LEU D 396 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG D 405 " --> pdb=" O CYS D 401 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL D 406 " --> pdb=" O ALA D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 429 Processing helix chain 'D' and resid 536 through 547 removed outlier: 3.654A pdb=" N GLU D 540 " --> pdb=" O GLU D 536 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL D 541 " --> pdb=" O GLN D 537 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL D 542 " --> pdb=" O ILE D 538 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR D 546 " --> pdb=" O VAL D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 569 removed outlier: 4.988A pdb=" N ALA D 565 " --> pdb=" O LEU D 561 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ASP D 566 " --> pdb=" O VAL D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 592 removed outlier: 3.785A pdb=" N GLY D 592 " --> pdb=" O ARG D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 625 removed outlier: 3.535A pdb=" N LEU D 616 " --> pdb=" O GLY D 612 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA D 617 " --> pdb=" O LYS D 613 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 643 No H-bonds generated for 'chain 'D' and resid 641 through 643' Processing helix chain 'D' and resid 644 through 649 Processing helix chain 'D' and resid 680 through 684 Processing helix chain 'D' and resid 685 through 690 Processing helix chain 'D' and resid 692 through 699 Processing helix chain 'D' and resid 723 through 730 removed outlier: 3.941A pdb=" N GLY D 730 " --> pdb=" O HIS D 726 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 752 Processing helix chain 'D' and resid 755 through 759 Processing helix chain 'D' and resid 770 through 791 removed outlier: 3.633A pdb=" N ASP D 784 " --> pdb=" O LEU D 780 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL D 785 " --> pdb=" O GLN D 781 " (cutoff:3.500A) Processing helix chain 'D' and resid 799 through 810 removed outlier: 3.649A pdb=" N SER D 810 " --> pdb=" O ILE D 806 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 838 removed outlier: 3.680A pdb=" N ARG D 821 " --> pdb=" O ALA D 817 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N THR D 830 " --> pdb=" O LYS D 826 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN D 838 " --> pdb=" O LYS D 834 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 179 removed outlier: 3.677A pdb=" N GLY E 178 " --> pdb=" O GLU E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 198 removed outlier: 3.954A pdb=" N ILE E 190 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER E 198 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 229 Processing helix chain 'E' and resid 232 through 236 Processing helix chain 'E' and resid 244 through 249 Processing helix chain 'E' and resid 255 through 269 Processing helix chain 'E' and resid 270 through 272 No H-bonds generated for 'chain 'E' and resid 270 through 272' Processing helix chain 'E' and resid 282 through 288 removed outlier: 3.752A pdb=" N VAL E 286 " --> pdb=" O GLU E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 309 Proline residue: E 304 - end of helix Processing helix chain 'E' and resid 318 through 325 removed outlier: 3.591A pdb=" N TYR E 322 " --> pdb=" O THR E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 335 removed outlier: 3.518A pdb=" N ARG E 335 " --> pdb=" O PHE E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 365 removed outlier: 3.549A pdb=" N THR E 349 " --> pdb=" O SER E 345 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE E 350 " --> pdb=" O VAL E 346 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER E 351 " --> pdb=" O PRO E 347 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU E 358 " --> pdb=" O ARG E 354 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LYS E 359 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR E 360 " --> pdb=" O LEU E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 380 Processing helix chain 'E' and resid 389 through 391 No H-bonds generated for 'chain 'E' and resid 389 through 391' Processing helix chain 'E' and resid 392 through 409 removed outlier: 3.712A pdb=" N LEU E 396 " --> pdb=" O LYS E 392 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA E 400 " --> pdb=" O LEU E 396 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG E 405 " --> pdb=" O CYS E 401 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL E 406 " --> pdb=" O ALA E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 429 Processing helix chain 'E' and resid 536 through 547 removed outlier: 3.684A pdb=" N VAL E 541 " --> pdb=" O GLN E 537 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL E 542 " --> pdb=" O ILE E 538 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR E 546 " --> pdb=" O VAL E 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 554 through 569 removed outlier: 4.940A pdb=" N ALA E 565 " --> pdb=" O LEU E 561 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ASP E 566 " --> pdb=" O VAL E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 592 removed outlier: 3.807A pdb=" N GLY E 592 " --> pdb=" O ARG E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 625 removed outlier: 3.529A pdb=" N LEU E 616 " --> pdb=" O GLY E 612 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA E 617 " --> pdb=" O LYS E 613 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE E 625 " --> pdb=" O ALA E 621 " (cutoff:3.500A) Processing helix chain 'E' and resid 641 through 643 No H-bonds generated for 'chain 'E' and resid 641 through 643' Processing helix chain 'E' and resid 644 through 649 Processing helix chain 'E' and resid 680 through 684 Processing helix chain 'E' and resid 685 through 690 Processing helix chain 'E' and resid 692 through 699 removed outlier: 3.596A pdb=" N LEU E 696 " --> pdb=" O LEU E 692 " (cutoff:3.500A) Processing helix chain 'E' and resid 723 through 730 removed outlier: 3.902A pdb=" N GLY E 730 " --> pdb=" O HIS E 726 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 752 Processing helix chain 'E' and resid 755 through 760 removed outlier: 4.147A pdb=" N ARG E 759 " --> pdb=" O GLU E 755 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU E 760 " --> pdb=" O LEU E 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 755 through 760' Processing helix chain 'E' and resid 770 through 791 removed outlier: 3.748A pdb=" N ASP E 784 " --> pdb=" O LEU E 780 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL E 785 " --> pdb=" O GLN E 781 " (cutoff:3.500A) Processing helix chain 'E' and resid 799 through 810 removed outlier: 3.563A pdb=" N LEU E 803 " --> pdb=" O THR E 799 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER E 810 " --> pdb=" O ILE E 806 " (cutoff:3.500A) Processing helix chain 'E' and resid 817 through 838 removed outlier: 3.709A pdb=" N ARG E 821 " --> pdb=" O ALA E 817 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR E 830 " --> pdb=" O LYS E 826 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN E 838 " --> pdb=" O LYS E 834 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 179 removed outlier: 3.549A pdb=" N ALA F 177 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY F 178 " --> pdb=" O GLU F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 198 removed outlier: 3.942A pdb=" N ILE F 190 " --> pdb=" O ARG F 186 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG F 191 " --> pdb=" O ASP F 187 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER F 198 " --> pdb=" O VAL F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 229 Processing helix chain 'F' and resid 232 through 236 Processing helix chain 'F' and resid 244 through 249 Processing helix chain 'F' and resid 255 through 269 Processing helix chain 'F' and resid 270 through 272 No H-bonds generated for 'chain 'F' and resid 270 through 272' Processing helix chain 'F' and resid 282 through 288 removed outlier: 3.697A pdb=" N VAL F 286 " --> pdb=" O GLU F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 309 Proline residue: F 304 - end of helix Processing helix chain 'F' and resid 318 through 325 Processing helix chain 'F' and resid 326 through 329 removed outlier: 3.690A pdb=" N ASP F 329 " --> pdb=" O VAL F 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 326 through 329' Processing helix chain 'F' and resid 331 through 335 Processing helix chain 'F' and resid 345 through 365 removed outlier: 3.553A pdb=" N THR F 349 " --> pdb=" O SER F 345 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE F 350 " --> pdb=" O VAL F 346 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER F 351 " --> pdb=" O PRO F 347 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU F 358 " --> pdb=" O ARG F 354 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LYS F 359 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR F 360 " --> pdb=" O LEU F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 380 Processing helix chain 'F' and resid 389 through 391 No H-bonds generated for 'chain 'F' and resid 389 through 391' Processing helix chain 'F' and resid 392 through 409 removed outlier: 3.680A pdb=" N LEU F 396 " --> pdb=" O LYS F 392 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA F 400 " --> pdb=" O LEU F 396 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG F 405 " --> pdb=" O CYS F 401 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 429 Processing helix chain 'F' and resid 536 through 547 removed outlier: 3.507A pdb=" N GLU F 540 " --> pdb=" O GLU F 536 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL F 541 " --> pdb=" O GLN F 537 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL F 542 " --> pdb=" O ILE F 538 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR F 546 " --> pdb=" O VAL F 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 554 through 569 removed outlier: 4.894A pdb=" N ALA F 565 " --> pdb=" O LEU F 561 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ASP F 566 " --> pdb=" O VAL F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 575 through 592 removed outlier: 3.803A pdb=" N GLY F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 625 removed outlier: 3.514A pdb=" N LEU F 616 " --> pdb=" O GLY F 612 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA F 617 " --> pdb=" O LYS F 613 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE F 625 " --> pdb=" O ALA F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 643 No H-bonds generated for 'chain 'F' and resid 641 through 643' Processing helix chain 'F' and resid 644 through 649 Processing helix chain 'F' and resid 680 through 684 Processing helix chain 'F' and resid 685 through 690 Processing helix chain 'F' and resid 692 through 699 removed outlier: 3.670A pdb=" N LEU F 696 " --> pdb=" O LEU F 692 " (cutoff:3.500A) Processing helix chain 'F' and resid 723 through 730 removed outlier: 4.186A pdb=" N GLY F 730 " --> pdb=" O HIS F 726 " (cutoff:3.500A) Processing helix chain 'F' and resid 737 through 752 Processing helix chain 'F' and resid 755 through 759 Processing helix chain 'F' and resid 770 through 791 removed outlier: 3.639A pdb=" N ASP F 784 " --> pdb=" O LEU F 780 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL F 785 " --> pdb=" O GLN F 781 " (cutoff:3.500A) Processing helix chain 'F' and resid 799 through 810 removed outlier: 3.686A pdb=" N SER F 810 " --> pdb=" O ILE F 806 " (cutoff:3.500A) Processing helix chain 'F' and resid 817 through 838 removed outlier: 3.696A pdb=" N ARG F 821 " --> pdb=" O ALA F 817 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N THR F 830 " --> pdb=" O LYS F 826 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN F 838 " --> pdb=" O LYS F 834 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 179 removed outlier: 3.620A pdb=" N ALA G 177 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY G 178 " --> pdb=" O GLU G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 198 removed outlier: 3.943A pdb=" N ILE G 190 " --> pdb=" O ARG G 186 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG G 191 " --> pdb=" O ASP G 187 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER G 198 " --> pdb=" O VAL G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 229 Processing helix chain 'G' and resid 232 through 236 Processing helix chain 'G' and resid 244 through 249 Processing helix chain 'G' and resid 255 through 270 removed outlier: 3.784A pdb=" N GLU G 270 " --> pdb=" O LEU G 266 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 288 removed outlier: 3.878A pdb=" N VAL G 286 " --> pdb=" O GLU G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 309 Proline residue: G 304 - end of helix Processing helix chain 'G' and resid 318 through 325 removed outlier: 3.567A pdb=" N TYR G 322 " --> pdb=" O THR G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 335 removed outlier: 3.509A pdb=" N ARG G 335 " --> pdb=" O PHE G 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 365 removed outlier: 3.633A pdb=" N THR G 349 " --> pdb=" O SER G 345 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE G 350 " --> pdb=" O VAL G 346 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER G 351 " --> pdb=" O PRO G 347 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU G 358 " --> pdb=" O ARG G 354 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LYS G 359 " --> pdb=" O GLY G 355 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR G 360 " --> pdb=" O LEU G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 380 removed outlier: 3.790A pdb=" N LEU G 373 " --> pdb=" O GLN G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 392 through 409 removed outlier: 3.716A pdb=" N LEU G 396 " --> pdb=" O LYS G 392 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA G 400 " --> pdb=" O LEU G 396 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG G 405 " --> pdb=" O CYS G 401 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL G 406 " --> pdb=" O ALA G 402 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 429 Processing helix chain 'G' and resid 536 through 547 removed outlier: 3.511A pdb=" N GLU G 540 " --> pdb=" O GLU G 536 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL G 541 " --> pdb=" O GLN G 537 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL G 542 " --> pdb=" O ILE G 538 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR G 546 " --> pdb=" O VAL G 542 " (cutoff:3.500A) Processing helix chain 'G' and resid 554 through 563 Processing helix chain 'G' and resid 563 through 569 Processing helix chain 'G' and resid 575 through 592 removed outlier: 3.805A pdb=" N GLY G 592 " --> pdb=" O ARG G 588 " (cutoff:3.500A) Processing helix chain 'G' and resid 612 through 625 removed outlier: 3.523A pdb=" N LEU G 616 " --> pdb=" O GLY G 612 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA G 617 " --> pdb=" O LYS G 613 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE G 625 " --> pdb=" O ALA G 621 " (cutoff:3.500A) Processing helix chain 'G' and resid 641 through 643 No H-bonds generated for 'chain 'G' and resid 641 through 643' Processing helix chain 'G' and resid 644 through 649 Processing helix chain 'G' and resid 680 through 684 Processing helix chain 'G' and resid 685 through 690 Processing helix chain 'G' and resid 692 through 699 removed outlier: 3.554A pdb=" N LEU G 696 " --> pdb=" O LEU G 692 " (cutoff:3.500A) Processing helix chain 'G' and resid 723 through 730 removed outlier: 4.238A pdb=" N GLY G 730 " --> pdb=" O HIS G 726 " (cutoff:3.500A) Processing helix chain 'G' and resid 737 through 752 Processing helix chain 'G' and resid 755 through 759 Processing helix chain 'G' and resid 770 through 791 removed outlier: 3.622A pdb=" N ASP G 784 " --> pdb=" O LEU G 780 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL G 785 " --> pdb=" O GLN G 781 " (cutoff:3.500A) Processing helix chain 'G' and resid 799 through 810 removed outlier: 3.668A pdb=" N SER G 810 " --> pdb=" O ILE G 806 " (cutoff:3.500A) Processing helix chain 'G' and resid 817 through 838 removed outlier: 3.626A pdb=" N ARG G 821 " --> pdb=" O ALA G 817 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR G 830 " --> pdb=" O LYS G 826 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN G 838 " --> pdb=" O LYS G 834 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 171 through 172 removed outlier: 6.700A pdb=" N ARG A 239 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N PHE A 279 " --> pdb=" O ARG A 239 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE A 241 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG A 312 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA A 316 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 315 " --> pdb=" O PRO A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 716 through 720 removed outlier: 6.302A pdb=" N PHE A 603 " --> pdb=" O MET A 718 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N SER A 720 " --> pdb=" O PHE A 603 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE A 605 " --> pdb=" O SER A 720 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N SER A 602 " --> pdb=" O GLU A 762 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N VAL A 764 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU A 604 " --> pdb=" O VAL A 764 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 632 through 633 removed outlier: 6.542A pdb=" N VAL A 632 " --> pdb=" O LEU A 677 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 701 through 702 Processing sheet with id=AA5, first strand: chain 'A' and resid 795 through 797 removed outlier: 7.006A pdb=" N ALA A 795 " --> pdb=" O VAL A 847 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N ILE A 849 " --> pdb=" O ALA A 795 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ALA A 797 " --> pdb=" O ILE A 849 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP A 850 " --> pdb=" O ALA A 859 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 171 through 172 removed outlier: 6.763A pdb=" N ARG B 239 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N PHE B 279 " --> pdb=" O ARG B 239 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE B 241 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG B 312 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA B 316 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N THR B 317 " --> pdb=" O PRO B 205 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU B 207 " --> pdb=" O THR B 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 632 through 633 removed outlier: 6.535A pdb=" N VAL B 632 " --> pdb=" O LEU B 677 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE B 676 " --> pdb=" O ILE B 717 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N THR B 719 " --> pdb=" O ILE B 676 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE B 603 " --> pdb=" O MET B 718 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N SER B 720 " --> pdb=" O PHE B 603 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N PHE B 605 " --> pdb=" O SER B 720 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER B 602 " --> pdb=" O GLU B 762 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N VAL B 764 " --> pdb=" O SER B 602 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU B 604 " --> pdb=" O VAL B 764 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 701 through 702 Processing sheet with id=AA9, first strand: chain 'B' and resid 795 through 797 removed outlier: 6.880A pdb=" N ALA B 795 " --> pdb=" O VAL B 847 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N ILE B 849 " --> pdb=" O ALA B 795 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ALA B 797 " --> pdb=" O ILE B 849 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP B 850 " --> pdb=" O ALA B 859 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 171 through 172 removed outlier: 3.859A pdb=" N ILE C 277 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 241 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ARG C 312 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA C 316 " --> pdb=" O ILE C 280 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU C 207 " --> pdb=" O THR C 317 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 632 through 633 removed outlier: 6.600A pdb=" N VAL C 632 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE C 676 " --> pdb=" O ILE C 717 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N THR C 719 " --> pdb=" O ILE C 676 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE C 603 " --> pdb=" O MET C 718 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER C 720 " --> pdb=" O PHE C 603 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE C 605 " --> pdb=" O SER C 720 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N SER C 602 " --> pdb=" O GLU C 762 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL C 764 " --> pdb=" O SER C 602 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU C 604 " --> pdb=" O VAL C 764 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 701 through 702 Processing sheet with id=AB4, first strand: chain 'C' and resid 795 through 797 removed outlier: 6.887A pdb=" N ALA C 795 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N ILE C 849 " --> pdb=" O ALA C 795 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ALA C 797 " --> pdb=" O ILE C 849 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP C 850 " --> pdb=" O ALA C 859 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 171 through 172 removed outlier: 4.791A pdb=" N ARG D 312 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA D 316 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N THR D 317 " --> pdb=" O PRO D 205 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU D 207 " --> pdb=" O THR D 317 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 632 through 633 removed outlier: 6.550A pdb=" N VAL D 632 " --> pdb=" O LEU D 677 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE D 676 " --> pdb=" O ILE D 717 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N THR D 719 " --> pdb=" O ILE D 676 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE D 603 " --> pdb=" O MET D 718 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N SER D 720 " --> pdb=" O PHE D 603 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE D 605 " --> pdb=" O SER D 720 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SER D 602 " --> pdb=" O GLU D 762 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N VAL D 764 " --> pdb=" O SER D 602 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU D 604 " --> pdb=" O VAL D 764 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 701 through 702 Processing sheet with id=AB8, first strand: chain 'D' and resid 795 through 797 removed outlier: 6.917A pdb=" N ALA D 795 " --> pdb=" O VAL D 847 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N ILE D 849 " --> pdb=" O ALA D 795 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ALA D 797 " --> pdb=" O ILE D 849 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP D 850 " --> pdb=" O ALA D 859 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 171 through 172 removed outlier: 6.661A pdb=" N ARG E 239 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE E 279 " --> pdb=" O ARG E 239 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE E 241 " --> pdb=" O PHE E 279 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ARG E 312 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY E 315 " --> pdb=" O PRO E 205 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 632 through 633 removed outlier: 6.516A pdb=" N VAL E 632 " --> pdb=" O LEU E 677 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE E 676 " --> pdb=" O ILE E 717 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N THR E 719 " --> pdb=" O ILE E 676 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N PHE E 603 " --> pdb=" O MET E 718 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N SER E 720 " --> pdb=" O PHE E 603 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE E 605 " --> pdb=" O SER E 720 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER E 602 " --> pdb=" O GLU E 762 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL E 764 " --> pdb=" O SER E 602 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU E 604 " --> pdb=" O VAL E 764 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 701 through 702 Processing sheet with id=AC3, first strand: chain 'E' and resid 795 through 797 removed outlier: 6.877A pdb=" N ALA E 795 " --> pdb=" O VAL E 847 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N ILE E 849 " --> pdb=" O ALA E 795 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ALA E 797 " --> pdb=" O ILE E 849 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP E 850 " --> pdb=" O ALA E 859 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 171 through 172 removed outlier: 4.753A pdb=" N ARG F 312 " --> pdb=" O VAL F 276 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY F 315 " --> pdb=" O PRO F 205 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 716 through 720 removed outlier: 6.321A pdb=" N PHE F 603 " --> pdb=" O MET F 718 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N SER F 720 " --> pdb=" O PHE F 603 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N PHE F 605 " --> pdb=" O SER F 720 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER F 602 " --> pdb=" O GLU F 762 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N VAL F 764 " --> pdb=" O SER F 602 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU F 604 " --> pdb=" O VAL F 764 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 632 through 633 removed outlier: 6.537A pdb=" N VAL F 632 " --> pdb=" O LEU F 677 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 701 through 702 Processing sheet with id=AC8, first strand: chain 'F' and resid 795 through 797 removed outlier: 6.891A pdb=" N ALA F 795 " --> pdb=" O VAL F 847 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ILE F 849 " --> pdb=" O ALA F 795 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ALA F 797 " --> pdb=" O ILE F 849 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP F 850 " --> pdb=" O ALA F 859 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 171 through 172 removed outlier: 6.567A pdb=" N ARG G 239 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N PHE G 279 " --> pdb=" O ARG G 239 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE G 241 " --> pdb=" O PHE G 279 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG G 312 " --> pdb=" O VAL G 276 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA G 316 " --> pdb=" O ILE G 280 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N THR G 317 " --> pdb=" O PRO G 205 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU G 207 " --> pdb=" O THR G 317 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 632 through 633 removed outlier: 6.521A pdb=" N VAL G 632 " --> pdb=" O LEU G 677 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE G 676 " --> pdb=" O ILE G 717 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N THR G 719 " --> pdb=" O ILE G 676 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N PHE G 603 " --> pdb=" O MET G 718 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N SER G 720 " --> pdb=" O PHE G 603 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE G 605 " --> pdb=" O SER G 720 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N SER G 602 " --> pdb=" O GLU G 762 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL G 764 " --> pdb=" O SER G 602 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU G 604 " --> pdb=" O VAL G 764 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'G' and resid 701 through 702 Processing sheet with id=AD3, first strand: chain 'G' and resid 795 through 797 removed outlier: 6.892A pdb=" N ALA G 795 " --> pdb=" O VAL G 847 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N ILE G 849 " --> pdb=" O ALA G 795 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ALA G 797 " --> pdb=" O ILE G 849 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP G 850 " --> pdb=" O ALA G 859 " (cutoff:3.500A) 1405 hydrogen bonds defined for protein. 3963 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: 11.31 Time building geometry restraints manager: 8.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11151 1.34 - 1.46: 6271 1.46 - 1.58: 14848 1.58 - 1.70: 42 1.70 - 1.82: 175 Bond restraints: 32487 Sorted by residual: bond pdb=" CD GLU B 559 " pdb=" OE1 GLU B 559 " ideal model delta sigma weight residual 1.249 1.225 0.024 1.90e-02 2.77e+03 1.64e+00 bond pdb=" CB LYS B 267 " pdb=" CG LYS B 267 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.36e+00 bond pdb=" CG GLU B 559 " pdb=" CD GLU B 559 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.36e+00 bond pdb=" CA GLU E 680 " pdb=" CB GLU E 680 " ideal model delta sigma weight residual 1.527 1.546 -0.018 1.61e-02 3.86e+03 1.32e+00 bond pdb=" CB ASP A 237 " pdb=" CG ASP A 237 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.30e+00 ... (remaining 32482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 43314 2.70 - 5.40: 484 5.40 - 8.10: 101 8.10 - 10.80: 27 10.80 - 13.50: 6 Bond angle restraints: 43932 Sorted by residual: angle pdb=" C ARG D 387 " pdb=" CA ARG D 387 " pdb=" CB ARG D 387 " ideal model delta sigma weight residual 116.54 110.83 5.71 1.15e+00 7.56e-01 2.47e+01 angle pdb=" CB LYS B 267 " pdb=" CG LYS B 267 " pdb=" CD LYS B 267 " ideal model delta sigma weight residual 111.30 120.44 -9.14 2.30e+00 1.89e-01 1.58e+01 angle pdb=" CA LEU D 266 " pdb=" CB LEU D 266 " pdb=" CG LEU D 266 " ideal model delta sigma weight residual 116.30 129.80 -13.50 3.50e+00 8.16e-02 1.49e+01 angle pdb=" CA LYS E 267 " pdb=" CB LYS E 267 " pdb=" CG LYS E 267 " ideal model delta sigma weight residual 114.10 121.63 -7.53 2.00e+00 2.50e-01 1.42e+01 angle pdb=" CB MET E 640 " pdb=" CG MET E 640 " pdb=" SD MET E 640 " ideal model delta sigma weight residual 112.70 123.94 -11.24 3.00e+00 1.11e-01 1.40e+01 ... (remaining 43927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 16998 17.93 - 35.86: 2175 35.86 - 53.79: 612 53.79 - 71.72: 113 71.72 - 89.65: 59 Dihedral angle restraints: 19957 sinusoidal: 8414 harmonic: 11543 Sorted by residual: dihedral pdb=" C2' ADP B1002 " pdb=" C1' ADP B1002 " pdb=" N9 ADP B1002 " pdb=" C4 ADP B1002 " ideal model delta sinusoidal sigma weight residual 91.55 -179.21 -89.24 1 2.00e+01 2.50e-03 2.37e+01 dihedral pdb=" C2' ADP G1002 " pdb=" C1' ADP G1002 " pdb=" N9 ADP G1002 " pdb=" C4 ADP G1002 " ideal model delta sinusoidal sigma weight residual 91.55 -179.72 -88.74 1 2.00e+01 2.50e-03 2.35e+01 dihedral pdb=" C2' ADP C1002 " pdb=" C1' ADP C1002 " pdb=" N9 ADP C1002 " pdb=" C4 ADP C1002 " ideal model delta sinusoidal sigma weight residual 91.55 179.12 -87.57 1 2.00e+01 2.50e-03 2.30e+01 ... (remaining 19954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4546 0.070 - 0.140: 491 0.140 - 0.210: 18 0.210 - 0.280: 3 0.280 - 0.350: 3 Chirality restraints: 5061 Sorted by residual: chirality pdb=" CG LEU G 266 " pdb=" CB LEU G 266 " pdb=" CD1 LEU G 266 " pdb=" CD2 LEU G 266 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CG LEU B 180 " pdb=" CB LEU B 180 " pdb=" CD1 LEU B 180 " pdb=" CD2 LEU B 180 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CG LEU E 180 " pdb=" CB LEU E 180 " pdb=" CD1 LEU E 180 " pdb=" CD2 LEU E 180 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 5058 not shown) Planarity restraints: 5705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 680 " -0.011 2.00e-02 2.50e+03 2.32e-02 5.40e+00 pdb=" CD GLU D 680 " 0.040 2.00e-02 2.50e+03 pdb=" OE1 GLU D 680 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU D 680 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN D 598 " 0.037 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO D 599 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO D 599 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 599 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 598 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.66e+00 pdb=" N PRO B 599 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 599 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 599 " 0.030 5.00e-02 4.00e+02 ... (remaining 5702 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 486 2.68 - 3.23: 30958 3.23 - 3.79: 47124 3.79 - 4.34: 56511 4.34 - 4.90: 92991 Nonbonded interactions: 228070 Sorted by model distance: nonbonded pdb=" OG1 THR A 665 " pdb=" OE1 GLU A 666 " model vdw 2.121 3.040 nonbonded pdb=" OG1 THR C 665 " pdb=" OE1 GLU C 666 " model vdw 2.148 3.040 nonbonded pdb=" O ALA F 376 " pdb=" OG SER F 380 " model vdw 2.207 3.040 nonbonded pdb=" O ALA B 376 " pdb=" OG SER B 380 " model vdw 2.210 3.040 nonbonded pdb=" N GLU A 666 " pdb=" OE1 GLU A 666 " model vdw 2.211 3.120 ... (remaining 228065 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.250 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 63.970 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32487 Z= 0.127 Angle : 0.734 13.499 43932 Z= 0.337 Chirality : 0.044 0.350 5061 Planarity : 0.004 0.055 5705 Dihedral : 17.785 89.646 12481 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.00 % Favored : 93.85 % Rotamer: Outliers : 0.30 % Allowed : 28.42 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.14), residues: 3934 helix: 0.77 (0.12), residues: 1953 sheet: 0.66 (0.23), residues: 574 loop : -1.20 (0.18), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 823 HIS 0.014 0.001 HIS C 429 PHE 0.019 0.001 PHE A 689 TYR 0.018 0.001 TYR C 325 ARG 0.014 0.000 ARG F 323 Details of bonding type rmsd hydrogen bonds : bond 0.15941 ( 1405) hydrogen bonds : angle 5.56458 ( 3963) covalent geometry : bond 0.00279 (32487) covalent geometry : angle 0.73368 (43932) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7868 Ramachandran restraints generated. 3934 Oldfield, 0 Emsley, 3934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7868 Ramachandran restraints generated. 3934 Oldfield, 0 Emsley, 3934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 310 time to evaluate : 4.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 317 average time/residue: 0.4155 time to fit residues: 219.5279 Evaluate side-chains 301 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 294 time to evaluate : 3.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain C residue 429 HIS Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 765 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 336 optimal weight: 0.7980 chunk 302 optimal weight: 2.9990 chunk 167 optimal weight: 0.7980 chunk 103 optimal weight: 8.9990 chunk 203 optimal weight: 8.9990 chunk 161 optimal weight: 2.9990 chunk 312 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 190 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 362 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** 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 = 0.3838 r_free = 0.3838 target = 0.140039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111202 restraints weight = 60675.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.110220 restraints weight = 74594.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.111734 restraints weight = 72956.105| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 32487 Z= 0.155 Angle : 0.670 9.032 43932 Z= 0.311 Chirality : 0.044 0.261 5061 Planarity : 0.005 0.059 5705 Dihedral : 6.495 92.858 4619 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.82 % Favored : 94.03 % Rotamer: Outliers : 3.76 % Allowed : 26.32 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3934 helix: 0.79 (0.12), residues: 2002 sheet: 0.41 (0.23), residues: 532 loop : -1.19 (0.18), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 823 HIS 0.006 0.001 HIS B 284 PHE 0.017 0.001 PHE F 258 TYR 0.008 0.001 TYR C 322 ARG 0.006 0.000 ARG F 323 Details of bonding type rmsd hydrogen bonds : bond 0.04379 ( 1405) hydrogen bonds : angle 4.66307 ( 3963) covalent geometry : bond 0.00364 (32487) covalent geometry : angle 0.66970 (43932) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7868 Ramachandran restraints generated. 3934 Oldfield, 0 Emsley, 3934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7868 Ramachandran restraints generated. 3934 Oldfield, 0 Emsley, 3934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 330 time to evaluate : 3.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 ASN cc_start: 0.6633 (OUTLIER) cc_final: 0.6250 (p0) REVERT: B 323 ARG cc_start: 0.8231 (tmt170) cc_final: 0.8015 (ttp80) REVERT: B 665 THR cc_start: 0.8378 (p) cc_final: 0.8118 (t) REVERT: C 323 ARG cc_start: 0.8204 (tmt170) cc_final: 0.7616 (ttp80) REVERT: D 665 THR cc_start: 0.8435 (p) cc_final: 0.8149 (t) REVERT: D 752 PHE cc_start: 0.7168 (OUTLIER) cc_final: 0.6788 (m-80) REVERT: E 559 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8441 (pm20) REVERT: E 665 THR cc_start: 0.8383 (p) cc_final: 0.8149 (t) REVERT: E 752 PHE cc_start: 0.6810 (OUTLIER) cc_final: 0.6477 (m-10) REVERT: G 323 ARG cc_start: 0.8572 (tmt170) cc_final: 0.8075 (ttp80) REVERT: G 752 PHE cc_start: 0.6816 (OUTLIER) cc_final: 0.5699 (m-80) outliers start: 127 outliers final: 80 residues processed: 424 average time/residue: 0.4272 time to fit residues: 301.6587 Evaluate side-chains 384 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 299 time to evaluate : 4.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 697 ASP Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 695 VAL Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 718 MET Chi-restraints excluded: chain C residue 757 LEU Chi-restraints excluded: chain C residue 763 ILE Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 697 ASP Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 752 PHE Chi-restraints excluded: chain D residue 763 ILE Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 824 ILE Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 401 CYS Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 559 GLU Chi-restraints excluded: chain E residue 695 VAL Chi-restraints excluded: chain E residue 722 LEU Chi-restraints excluded: chain E residue 752 PHE Chi-restraints excluded: chain E residue 763 ILE Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain E residue 837 ILE Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 757 LEU Chi-restraints excluded: chain F residue 763 ILE Chi-restraints excluded: chain F residue 796 LEU Chi-restraints excluded: chain F residue 807 LEU Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain G residue 429 HIS Chi-restraints excluded: chain G residue 541 VAL Chi-restraints excluded: chain G residue 556 ASN Chi-restraints excluded: chain G residue 559 GLU Chi-restraints excluded: chain G residue 692 LEU Chi-restraints excluded: chain G residue 718 MET Chi-restraints excluded: chain G residue 722 LEU Chi-restraints excluded: chain G residue 752 PHE Chi-restraints excluded: chain G residue 757 LEU Chi-restraints excluded: chain G residue 760 LEU Chi-restraints excluded: chain G residue 763 ILE Chi-restraints excluded: chain G residue 796 LEU Chi-restraints excluded: chain G residue 807 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 387 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 343 optimal weight: 8.9990 chunk 376 optimal weight: 4.9990 chunk 260 optimal weight: 0.9980 chunk 325 optimal weight: 5.9990 chunk 224 optimal weight: 4.9990 chunk 283 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 GLN E 310 GLN ** G 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.139043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.110369 restraints weight = 60298.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.111029 restraints weight = 83148.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.111733 restraints weight = 75232.588| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 32487 Z= 0.172 Angle : 0.684 10.638 43932 Z= 0.319 Chirality : 0.044 0.236 5061 Planarity : 0.005 0.063 5705 Dihedral : 6.579 93.971 4608 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.46 % Favored : 93.37 % Rotamer: Outliers : 5.53 % Allowed : 26.26 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3934 helix: 0.73 (0.12), residues: 2002 sheet: 0.19 (0.22), residues: 567 loop : -1.25 (0.19), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 823 HIS 0.008 0.001 HIS G 388 PHE 0.011 0.001 PHE B 258 TYR 0.010 0.001 TYR F 655 ARG 0.008 0.000 ARG F 323 Details of bonding type rmsd hydrogen bonds : bond 0.04601 ( 1405) hydrogen bonds : angle 4.55489 ( 3963) covalent geometry : bond 0.00406 (32487) covalent geometry : angle 0.68450 (43932) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7868 Ramachandran restraints generated. 3934 Oldfield, 0 Emsley, 3934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7868 Ramachandran restraints generated. 3934 Oldfield, 0 Emsley, 3934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 318 time to evaluate : 3.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7820 (mm) REVERT: B 428 GLU cc_start: 0.7566 (pt0) cc_final: 0.7189 (pt0) REVERT: C 323 ARG cc_start: 0.7996 (tmt170) cc_final: 0.7726 (ttp80) REVERT: C 752 PHE cc_start: 0.6633 (OUTLIER) cc_final: 0.6387 (m-80) REVERT: D 665 THR cc_start: 0.8324 (p) cc_final: 0.8059 (t) REVERT: D 752 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6764 (m-80) REVERT: E 544 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7364 (ppt170) REVERT: E 559 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8326 (pp20) REVERT: E 752 PHE cc_start: 0.6837 (OUTLIER) cc_final: 0.6373 (m-80) REVERT: F 692 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.7472 (tt) REVERT: F 697 ASP cc_start: 0.6600 (t70) cc_final: 0.6225 (t70) REVERT: G 544 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7637 (ppt170) REVERT: G 752 PHE cc_start: 0.6808 (OUTLIER) cc_final: 0.5731 (m-80) outliers start: 187 outliers final: 141 residues processed: 463 average time/residue: 0.5035 time to fit residues: 385.9655 Evaluate side-chains 434 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 284 time to evaluate : 5.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 401 CYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 614 THR Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 401 CYS Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 695 VAL Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 718 MET Chi-restraints excluded: chain C residue 752 PHE Chi-restraints excluded: chain C residue 757 LEU Chi-restraints excluded: chain C residue 763 ILE Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 824 ILE Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 332 PHE Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 401 CYS Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 614 THR Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 697 ASP Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 752 PHE Chi-restraints excluded: chain D residue 757 LEU Chi-restraints excluded: chain D residue 763 ILE Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 824 ILE Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 401 CYS Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 544 ARG Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain E residue 559 GLU Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain E residue 695 VAL Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 722 LEU Chi-restraints excluded: chain E residue 752 PHE Chi-restraints excluded: chain E residue 757 LEU Chi-restraints excluded: chain E residue 763 ILE Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain E residue 837 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain F residue 614 THR Chi-restraints excluded: chain F residue 631 LEU Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 757 LEU Chi-restraints excluded: chain F residue 763 ILE Chi-restraints excluded: chain F residue 796 LEU Chi-restraints excluded: chain F residue 807 LEU Chi-restraints excluded: chain F residue 824 ILE Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain G residue 401 CYS Chi-restraints excluded: chain G residue 429 HIS Chi-restraints excluded: chain G residue 541 VAL Chi-restraints excluded: chain G residue 544 ARG Chi-restraints excluded: chain G residue 556 ASN Chi-restraints excluded: chain G residue 559 GLU Chi-restraints excluded: chain G residue 614 THR Chi-restraints excluded: chain G residue 692 LEU Chi-restraints excluded: chain G residue 695 VAL Chi-restraints excluded: chain G residue 722 LEU Chi-restraints excluded: chain G residue 752 PHE Chi-restraints excluded: chain G residue 763 ILE Chi-restraints excluded: chain G residue 796 LEU Chi-restraints excluded: chain G residue 807 LEU Chi-restraints excluded: chain G residue 837 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 382 optimal weight: 3.9990 chunk 267 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 0.3980 chunk 131 optimal weight: 2.9990 chunk 180 optimal weight: 20.0000 chunk 239 optimal weight: 20.0000 chunk 130 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 429 HIS ** 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 = 0.3820 r_free = 0.3820 target = 0.139228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.111271 restraints weight = 60113.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.113176 restraints weight = 81679.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.113644 restraints weight = 68881.567| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 32487 Z= 0.150 Angle : 0.672 12.594 43932 Z= 0.310 Chirality : 0.043 0.249 5061 Planarity : 0.004 0.061 5705 Dihedral : 6.580 93.787 4608 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.08 % Favored : 93.75 % Rotamer: Outliers : 5.26 % Allowed : 27.15 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3934 helix: 0.70 (0.12), residues: 2002 sheet: 0.15 (0.22), residues: 567 loop : -1.24 (0.19), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 823 HIS 0.005 0.001 HIS E 388 PHE 0.013 0.001 PHE D 258 TYR 0.008 0.001 TYR C 639 ARG 0.007 0.000 ARG F 323 Details of bonding type rmsd hydrogen bonds : bond 0.04244 ( 1405) hydrogen bonds : angle 4.48193 ( 3963) covalent geometry : bond 0.00353 (32487) covalent geometry : angle 0.67213 (43932) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7868 Ramachandran restraints generated. 3934 Oldfield, 0 Emsley, 3934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7868 Ramachandran restraints generated. 3934 Oldfield, 0 Emsley, 3934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 312 time to evaluate : 3.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.7582 (tpp) cc_final: 0.7266 (tpp) REVERT: B 323 ARG cc_start: 0.8374 (tmt170) cc_final: 0.7939 (ttp80) REVERT: B 428 GLU cc_start: 0.7681 (pt0) cc_final: 0.7285 (pt0) REVERT: B 544 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7857 (ppt170) REVERT: B 752 PHE cc_start: 0.7007 (OUTLIER) cc_final: 0.6375 (m-80) REVERT: C 323 ARG cc_start: 0.7990 (tmt170) cc_final: 0.7749 (ttp80) REVERT: C 752 PHE cc_start: 0.6539 (OUTLIER) cc_final: 0.6299 (m-10) REVERT: C 760 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8415 (mm) REVERT: D 305 MET cc_start: 0.7962 (pmm) cc_final: 0.7739 (pmm) REVERT: D 640 MET cc_start: 0.7340 (mmm) cc_final: 0.7122 (tpt) REVERT: D 665 THR cc_start: 0.8379 (p) cc_final: 0.8101 (t) REVERT: D 752 PHE cc_start: 0.7085 (OUTLIER) cc_final: 0.6661 (m-80) REVERT: E 752 PHE cc_start: 0.6776 (OUTLIER) cc_final: 0.6143 (m-80) REVERT: F 692 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.7492 (tt) REVERT: F 697 ASP cc_start: 0.6604 (t70) cc_final: 0.6236 (t70) REVERT: G 323 ARG cc_start: 0.8441 (tmt170) cc_final: 0.7902 (ttp80) REVERT: G 544 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7725 (ppt170) REVERT: G 752 PHE cc_start: 0.6636 (OUTLIER) cc_final: 0.5452 (m-80) outliers start: 178 outliers final: 137 residues processed: 450 average time/residue: 0.4360 time to fit residues: 327.1409 Evaluate side-chains 433 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 287 time to evaluate : 3.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 401 CYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 544 ARG Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 614 THR Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 695 VAL Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 718 MET Chi-restraints excluded: chain C residue 752 PHE Chi-restraints excluded: chain C residue 757 LEU Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 763 ILE Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 401 CYS Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 614 THR Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 752 PHE Chi-restraints excluded: chain D residue 757 LEU Chi-restraints excluded: chain D residue 763 ILE Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 824 ILE Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 401 CYS Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 556 ASN Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain E residue 692 LEU Chi-restraints excluded: chain E residue 695 VAL Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain E residue 722 LEU Chi-restraints excluded: chain E residue 752 PHE Chi-restraints excluded: chain E residue 757 LEU Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain E residue 837 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain F residue 401 CYS Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain F residue 544 ARG Chi-restraints excluded: chain F residue 614 THR Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 696 LEU Chi-restraints excluded: chain F residue 757 LEU Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 796 LEU Chi-restraints excluded: chain F residue 807 LEU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain G residue 401 CYS Chi-restraints excluded: chain G residue 429 HIS Chi-restraints excluded: chain G residue 541 VAL Chi-restraints excluded: chain G residue 544 ARG Chi-restraints excluded: chain G residue 556 ASN Chi-restraints excluded: chain G residue 559 GLU Chi-restraints excluded: chain G residue 614 THR Chi-restraints excluded: chain G residue 692 LEU Chi-restraints excluded: chain G residue 695 VAL Chi-restraints excluded: chain G residue 722 LEU Chi-restraints excluded: chain G residue 752 PHE Chi-restraints excluded: chain G residue 760 LEU Chi-restraints excluded: chain G residue 796 LEU Chi-restraints excluded: chain G residue 807 LEU Chi-restraints excluded: chain G residue 824 ILE Chi-restraints excluded: chain G residue 837 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 311 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 110 optimal weight: 0.2980 chunk 154 optimal weight: 0.5980 chunk 156 optimal weight: 0.0980 chunk 77 optimal weight: 5.9990 chunk 378 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 192 optimal weight: 9.9990 chunk 173 optimal weight: 0.9980 chunk 396 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 694 GLN C 310 GLN ** G 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.140977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.112776 restraints weight = 59066.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.111317 restraints weight = 74953.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.113004 restraints weight = 81236.161| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 32487 Z= 0.113 Angle : 0.656 12.486 43932 Z= 0.298 Chirality : 0.043 0.303 5061 Planarity : 0.004 0.057 5705 Dihedral : 6.435 91.515 4608 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.10 % Favored : 93.72 % Rotamer: Outliers : 4.91 % Allowed : 27.74 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.14), residues: 3934 helix: 0.72 (0.12), residues: 2002 sheet: 0.04 (0.25), residues: 441 loop : -1.04 (0.18), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 823 HIS 0.004 0.001 HIS F 388 PHE 0.009 0.001 PHE D 258 TYR 0.010 0.001 TYR E 655 ARG 0.008 0.000 ARG F 323 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 1405) hydrogen bonds : angle 4.40131 ( 3963) covalent geometry : bond 0.00252 (32487) covalent geometry : angle 0.65574 (43932) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7868 Ramachandran restraints generated. 3934 Oldfield, 0 Emsley, 3934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7868 Ramachandran restraints generated. 3934 Oldfield, 0 Emsley, 3934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 319 time to evaluate : 3.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LYS cc_start: 0.7548 (pttm) cc_final: 0.7154 (tmmt) REVERT: A 385 MET cc_start: 0.7632 (tpp) cc_final: 0.7344 (tpp) REVERT: A 692 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.7457 (tt) REVERT: B 323 ARG cc_start: 0.8426 (tmt170) cc_final: 0.8015 (ttp80) REVERT: B 428 GLU cc_start: 0.8026 (pt0) cc_final: 0.7531 (pt0) REVERT: B 544 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7897 (ppt170) REVERT: B 752 PHE cc_start: 0.6809 (OUTLIER) cc_final: 0.6208 (m-80) REVERT: D 665 THR cc_start: 0.8402 (p) cc_final: 0.8120 (t) REVERT: D 752 PHE cc_start: 0.6980 (OUTLIER) cc_final: 0.6438 (m-80) REVERT: E 614 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8794 (m) REVERT: E 752 PHE cc_start: 0.6727 (OUTLIER) cc_final: 0.5813 (m-80) REVERT: F 692 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.7502 (tt) REVERT: F 697 ASP cc_start: 0.6445 (t70) cc_final: 0.6129 (t70) REVERT: G 323 ARG cc_start: 0.8488 (tmt170) cc_final: 0.7971 (ttp80) REVERT: G 544 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7658 (ppt170) REVERT: G 692 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7941 (tp) outliers start: 166 outliers final: 123 residues processed: 447 average time/residue: 0.3835 time to fit residues: 285.9051 Evaluate side-chains 422 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 290 time to evaluate : 3.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 401 CYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 544 ARG Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 625 PHE Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 302 PHE Chi-restraints excluded: chain C residue 310 GLN Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 718 MET Chi-restraints excluded: chain C residue 757 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 824 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 401 CYS Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 697 ASP Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 752 PHE Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 824 ILE Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 401 CYS Chi-restraints excluded: chain E residue 556 ASN Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain E residue 625 PHE Chi-restraints excluded: chain E residue 692 LEU Chi-restraints excluded: chain E residue 695 VAL Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 745 MET Chi-restraints excluded: chain E residue 752 PHE Chi-restraints excluded: chain E residue 757 LEU Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain E residue 837 ILE Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain F residue 556 ASN Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 720 SER Chi-restraints excluded: chain F residue 757 LEU Chi-restraints excluded: chain F residue 763 ILE Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 796 LEU Chi-restraints excluded: chain F residue 807 LEU Chi-restraints excluded: chain F residue 824 ILE Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain G residue 401 CYS Chi-restraints excluded: chain G residue 541 VAL Chi-restraints excluded: chain G residue 544 ARG Chi-restraints excluded: chain G residue 556 ASN Chi-restraints excluded: chain G residue 614 THR Chi-restraints excluded: chain G residue 692 LEU Chi-restraints excluded: chain G residue 695 VAL Chi-restraints excluded: chain G residue 718 MET Chi-restraints excluded: chain G residue 760 LEU Chi-restraints excluded: chain G residue 796 LEU Chi-restraints excluded: chain G residue 807 LEU Chi-restraints excluded: chain G residue 837 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 155 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 191 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 236 optimal weight: 0.9990 chunk 137 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 429 HIS ** 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 = 0.3845 r_free = 0.3845 target = 0.141061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.113292 restraints weight = 59655.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.113314 restraints weight = 80051.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.114455 restraints weight = 77049.166| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 32487 Z= 0.115 Angle : 0.661 12.502 43932 Z= 0.299 Chirality : 0.042 0.311 5061 Planarity : 0.004 0.058 5705 Dihedral : 6.381 91.083 4608 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.97 % Favored : 93.85 % Rotamer: Outliers : 5.47 % Allowed : 27.60 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3934 helix: 0.70 (0.12), residues: 1995 sheet: 0.09 (0.25), residues: 441 loop : -0.98 (0.18), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 823 HIS 0.004 0.001 HIS F 388 PHE 0.013 0.001 PHE G 258 TYR 0.007 0.001 TYR G 325 ARG 0.010 0.000 ARG C 323 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 1405) hydrogen bonds : angle 4.35917 ( 3963) covalent geometry : bond 0.00261 (32487) covalent geometry : angle 0.66123 (43932) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7868 Ramachandran restraints generated. 3934 Oldfield, 0 Emsley, 3934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7868 Ramachandran restraints generated. 3934 Oldfield, 0 Emsley, 3934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 320 time to evaluate : 3.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LYS cc_start: 0.7392 (pttm) cc_final: 0.7026 (tmmt) REVERT: A 385 MET cc_start: 0.7601 (tpp) cc_final: 0.7349 (tpp) REVERT: A 692 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.7443 (tt) REVERT: B 428 GLU cc_start: 0.7932 (pt0) cc_final: 0.7437 (pt0) REVERT: B 544 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7900 (ppt170) REVERT: B 752 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.6241 (m-80) REVERT: B 771 HIS cc_start: 0.6686 (OUTLIER) cc_final: 0.6045 (m-70) REVERT: C 323 ARG cc_start: 0.8631 (ttp80) cc_final: 0.8249 (tmm160) REVERT: C 752 PHE cc_start: 0.7021 (OUTLIER) cc_final: 0.6749 (m-10) REVERT: C 760 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8292 (mm) REVERT: D 321 GLU cc_start: 0.7405 (mm-30) cc_final: 0.6976 (mm-30) REVERT: D 598 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7772 (mt0) REVERT: D 665 THR cc_start: 0.8301 (p) cc_final: 0.8011 (t) REVERT: D 752 PHE cc_start: 0.6949 (OUTLIER) cc_final: 0.6398 (m-80) REVERT: E 614 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8796 (m) REVERT: E 752 PHE cc_start: 0.6693 (OUTLIER) cc_final: 0.5767 (m-80) REVERT: F 317 THR cc_start: 0.8898 (t) cc_final: 0.8673 (m) REVERT: F 692 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.7485 (tt) REVERT: F 697 ASP cc_start: 0.6501 (t70) cc_final: 0.6176 (t70) REVERT: G 323 ARG cc_start: 0.8378 (tmt170) cc_final: 0.8024 (ttp80) REVERT: G 544 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7637 (ppt170) REVERT: G 692 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7877 (tp) REVERT: G 752 PHE cc_start: 0.6675 (OUTLIER) cc_final: 0.5573 (m-80) outliers start: 185 outliers final: 149 residues processed: 473 average time/residue: 0.4273 time to fit residues: 342.9604 Evaluate side-chains 467 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 304 time to evaluate : 2.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 401 CYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 544 ARG Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 625 PHE Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 697 ASP Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 771 HIS Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 695 VAL Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 718 MET Chi-restraints excluded: chain C residue 752 PHE Chi-restraints excluded: chain C residue 757 LEU Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 824 ILE Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 401 CYS Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 598 GLN Chi-restraints excluded: chain D residue 625 PHE Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 697 ASP Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain D residue 752 PHE Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 824 ILE Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 401 CYS Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 556 ASN Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain E residue 625 PHE Chi-restraints excluded: chain E residue 692 LEU Chi-restraints excluded: chain E residue 695 VAL Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain E residue 722 LEU Chi-restraints excluded: chain E residue 745 MET Chi-restraints excluded: chain E residue 752 PHE Chi-restraints excluded: chain E residue 757 LEU Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain E residue 837 ILE Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain F residue 544 ARG Chi-restraints excluded: chain F residue 556 ASN Chi-restraints excluded: chain F residue 625 PHE Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 720 SER Chi-restraints excluded: chain F residue 757 LEU Chi-restraints excluded: chain F residue 763 ILE Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 796 LEU Chi-restraints excluded: chain F residue 807 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain G residue 401 CYS Chi-restraints excluded: chain G residue 541 VAL Chi-restraints excluded: chain G residue 544 ARG Chi-restraints excluded: chain G residue 556 ASN Chi-restraints excluded: chain G residue 614 THR Chi-restraints excluded: chain G residue 625 PHE Chi-restraints excluded: chain G residue 692 LEU Chi-restraints excluded: chain G residue 695 VAL Chi-restraints excluded: chain G residue 718 MET Chi-restraints excluded: chain G residue 719 THR Chi-restraints excluded: chain G residue 752 PHE Chi-restraints excluded: chain G residue 760 LEU Chi-restraints excluded: chain G residue 763 ILE Chi-restraints excluded: chain G residue 796 LEU Chi-restraints excluded: chain G residue 807 LEU Chi-restraints excluded: chain G residue 824 ILE Chi-restraints excluded: chain G residue 837 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 51 optimal weight: 7.9990 chunk 270 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 149 optimal weight: 0.0060 chunk 141 optimal weight: 0.9990 chunk 259 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 chunk 324 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 114 optimal weight: 20.0000 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 429 HIS ** 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 = 0.3844 r_free = 0.3844 target = 0.140964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.112826 restraints weight = 59943.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111796 restraints weight = 77440.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.113248 restraints weight = 82042.972| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32487 Z= 0.124 Angle : 0.674 12.591 43932 Z= 0.304 Chirality : 0.043 0.237 5061 Planarity : 0.004 0.058 5705 Dihedral : 6.373 91.161 4608 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.15 % Favored : 93.67 % Rotamer: Outliers : 5.89 % Allowed : 27.51 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3934 helix: 0.67 (0.12), residues: 2002 sheet: -0.20 (0.24), residues: 511 loop : -0.87 (0.19), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 823 HIS 0.008 0.001 HIS A 388 PHE 0.011 0.001 PHE A 625 TYR 0.011 0.001 TYR C 655 ARG 0.008 0.000 ARG C 323 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 1405) hydrogen bonds : angle 4.32876 ( 3963) covalent geometry : bond 0.00286 (32487) covalent geometry : angle 0.67449 (43932) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7868 Ramachandran restraints generated. 3934 Oldfield, 0 Emsley, 3934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7868 Ramachandran restraints generated. 3934 Oldfield, 0 Emsley, 3934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 315 time to evaluate : 3.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LYS cc_start: 0.7505 (pttm) cc_final: 0.7111 (tmmt) REVERT: A 385 MET cc_start: 0.7490 (tpp) cc_final: 0.7273 (tpp) REVERT: A 692 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.7444 (tt) REVERT: A 771 HIS cc_start: 0.6600 (OUTLIER) cc_final: 0.6016 (m-70) REVERT: B 428 GLU cc_start: 0.8045 (pt0) cc_final: 0.7741 (pt0) REVERT: B 544 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7909 (ppt170) REVERT: B 752 PHE cc_start: 0.6875 (OUTLIER) cc_final: 0.6271 (m-80) REVERT: B 771 HIS cc_start: 0.6680 (OUTLIER) cc_final: 0.6101 (m-70) REVERT: C 752 PHE cc_start: 0.7026 (OUTLIER) cc_final: 0.6669 (m-10) REVERT: C 760 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8286 (mm) REVERT: D 598 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7882 (mt0) REVERT: D 640 MET cc_start: 0.7399 (mmm) cc_final: 0.7079 (tpt) REVERT: D 752 PHE cc_start: 0.6952 (OUTLIER) cc_final: 0.6469 (m-80) REVERT: E 614 THR cc_start: 0.9084 (OUTLIER) cc_final: 0.8755 (m) REVERT: E 692 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8143 (tp) REVERT: E 752 PHE cc_start: 0.6678 (OUTLIER) cc_final: 0.5695 (m-80) REVERT: F 692 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.7523 (tt) REVERT: F 697 ASP cc_start: 0.6432 (t70) cc_final: 0.6107 (t70) REVERT: F 771 HIS cc_start: 0.6582 (OUTLIER) cc_final: 0.6083 (m-70) REVERT: G 323 ARG cc_start: 0.8450 (tmt170) cc_final: 0.8142 (tmm-80) REVERT: G 544 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7638 (ppt170) REVERT: G 692 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7885 (tp) REVERT: G 752 PHE cc_start: 0.6684 (OUTLIER) cc_final: 0.5560 (m-80) outliers start: 199 outliers final: 157 residues processed: 478 average time/residue: 0.5343 time to fit residues: 432.1646 Evaluate side-chains 469 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 295 time to evaluate : 4.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 625 PHE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 771 HIS Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 401 CYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 544 ARG Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 614 THR Chi-restraints excluded: chain B residue 625 PHE Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 697 ASP Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 771 HIS Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 695 VAL Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 718 MET Chi-restraints excluded: chain C residue 752 PHE Chi-restraints excluded: chain C residue 757 LEU Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 763 ILE Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 824 ILE Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 401 CYS Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 598 GLN Chi-restraints excluded: chain D residue 614 THR Chi-restraints excluded: chain D residue 625 PHE Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain D residue 752 PHE Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 824 ILE Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 401 CYS Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 556 ASN Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain E residue 620 LEU Chi-restraints excluded: chain E residue 625 PHE Chi-restraints excluded: chain E residue 692 LEU Chi-restraints excluded: chain E residue 695 VAL Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 752 PHE Chi-restraints excluded: chain E residue 757 LEU Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain E residue 837 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain F residue 544 ARG Chi-restraints excluded: chain F residue 556 ASN Chi-restraints excluded: chain F residue 625 PHE Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 696 LEU Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 720 SER Chi-restraints excluded: chain F residue 757 LEU Chi-restraints excluded: chain F residue 763 ILE Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 771 HIS Chi-restraints excluded: chain F residue 796 LEU Chi-restraints excluded: chain F residue 807 LEU Chi-restraints excluded: chain F residue 824 ILE Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain G residue 401 CYS Chi-restraints excluded: chain G residue 541 VAL Chi-restraints excluded: chain G residue 544 ARG Chi-restraints excluded: chain G residue 556 ASN Chi-restraints excluded: chain G residue 614 THR Chi-restraints excluded: chain G residue 625 PHE Chi-restraints excluded: chain G residue 692 LEU Chi-restraints excluded: chain G residue 695 VAL Chi-restraints excluded: chain G residue 718 MET Chi-restraints excluded: chain G residue 719 THR Chi-restraints excluded: chain G residue 752 PHE Chi-restraints excluded: chain G residue 760 LEU Chi-restraints excluded: chain G residue 763 ILE Chi-restraints excluded: chain G residue 796 LEU Chi-restraints excluded: chain G residue 807 LEU Chi-restraints excluded: chain G residue 824 ILE Chi-restraints excluded: chain G residue 837 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 9 optimal weight: 20.0000 chunk 209 optimal weight: 0.4980 chunk 162 optimal weight: 10.0000 chunk 387 optimal weight: 7.9990 chunk 21 optimal weight: 0.0670 chunk 14 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 335 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 368 optimal weight: 4.9990 overall best weight: 2.5124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 338 GLN D 694 GLN G 429 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.139029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.110457 restraints weight = 59882.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110213 restraints weight = 78394.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.111547 restraints weight = 82901.868| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 32487 Z= 0.155 Angle : 0.708 12.497 43932 Z= 0.323 Chirality : 0.044 0.277 5061 Planarity : 0.004 0.061 5705 Dihedral : 6.525 93.272 4608 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.35 % Favored : 93.47 % Rotamer: Outliers : 5.89 % Allowed : 27.86 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.14), residues: 3934 helix: 0.65 (0.12), residues: 1995 sheet: 0.01 (0.21), residues: 637 loop : -0.97 (0.20), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 823 HIS 0.005 0.001 HIS C 284 PHE 0.011 0.001 PHE G 258 TYR 0.009 0.001 TYR C 639 ARG 0.011 0.000 ARG B 323 Details of bonding type rmsd hydrogen bonds : bond 0.04118 ( 1405) hydrogen bonds : angle 4.36986 ( 3963) covalent geometry : bond 0.00366 (32487) covalent geometry : angle 0.70786 (43932) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7868 Ramachandran restraints generated. 3934 Oldfield, 0 Emsley, 3934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7868 Ramachandran restraints generated. 3934 Oldfield, 0 Emsley, 3934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 298 time to evaluate : 4.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LYS cc_start: 0.7549 (pttm) cc_final: 0.7149 (tmmt) REVERT: A 385 MET cc_start: 0.7648 (tpp) cc_final: 0.7435 (tpp) REVERT: A 692 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.7401 (tt) REVERT: A 771 HIS cc_start: 0.6736 (OUTLIER) cc_final: 0.6139 (m-70) REVERT: B 428 GLU cc_start: 0.7867 (pt0) cc_final: 0.7439 (pt0) REVERT: B 544 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7891 (ppt170) REVERT: B 752 PHE cc_start: 0.6879 (OUTLIER) cc_final: 0.6328 (m-80) REVERT: B 771 HIS cc_start: 0.6889 (OUTLIER) cc_final: 0.6295 (m-70) REVERT: C 752 PHE cc_start: 0.6787 (OUTLIER) cc_final: 0.6466 (m-10) REVERT: C 760 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8344 (mm) REVERT: D 598 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7944 (mt0) REVERT: D 640 MET cc_start: 0.7410 (mmm) cc_final: 0.7189 (tpt) REVERT: D 752 PHE cc_start: 0.7038 (OUTLIER) cc_final: 0.6450 (m-80) REVERT: D 771 HIS cc_start: 0.6980 (OUTLIER) cc_final: 0.6349 (m-70) REVERT: E 752 PHE cc_start: 0.6747 (OUTLIER) cc_final: 0.5815 (m-80) REVERT: E 771 HIS cc_start: 0.6769 (OUTLIER) cc_final: 0.6309 (m-70) REVERT: F 428 GLU cc_start: 0.8125 (pt0) cc_final: 0.7921 (pt0) REVERT: F 692 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.7515 (tt) REVERT: F 697 ASP cc_start: 0.6536 (t70) cc_final: 0.6230 (t70) REVERT: F 771 HIS cc_start: 0.6813 (OUTLIER) cc_final: 0.6283 (m-70) REVERT: G 323 ARG cc_start: 0.8406 (tmt170) cc_final: 0.8120 (tmm-80) REVERT: G 544 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7773 (ppt170) REVERT: G 752 PHE cc_start: 0.6654 (OUTLIER) cc_final: 0.5478 (m-80) outliers start: 199 outliers final: 161 residues processed: 462 average time/residue: 0.4115 time to fit residues: 319.6809 Evaluate side-chains 466 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 289 time to evaluate : 3.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 771 HIS Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 401 CYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 544 ARG Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 614 THR Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 697 ASP Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 771 HIS Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 401 CYS Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 695 VAL Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 718 MET Chi-restraints excluded: chain C residue 752 PHE Chi-restraints excluded: chain C residue 757 LEU Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 763 ILE Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 824 ILE Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 401 CYS Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 559 GLU Chi-restraints excluded: chain D residue 598 GLN Chi-restraints excluded: chain D residue 614 THR Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain D residue 752 PHE Chi-restraints excluded: chain D residue 757 LEU Chi-restraints excluded: chain D residue 763 ILE Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 771 HIS Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 824 ILE Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 401 CYS Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 556 ASN Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain E residue 620 LEU Chi-restraints excluded: chain E residue 692 LEU Chi-restraints excluded: chain E residue 695 VAL Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 752 PHE Chi-restraints excluded: chain E residue 757 LEU Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain E residue 771 HIS Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain E residue 837 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain F residue 556 ASN Chi-restraints excluded: chain F residue 631 LEU Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 696 LEU Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 720 SER Chi-restraints excluded: chain F residue 763 ILE Chi-restraints excluded: chain F residue 771 HIS Chi-restraints excluded: chain F residue 796 LEU Chi-restraints excluded: chain F residue 807 LEU Chi-restraints excluded: chain F residue 824 ILE Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain G residue 401 CYS Chi-restraints excluded: chain G residue 541 VAL Chi-restraints excluded: chain G residue 544 ARG Chi-restraints excluded: chain G residue 556 ASN Chi-restraints excluded: chain G residue 614 THR Chi-restraints excluded: chain G residue 692 LEU Chi-restraints excluded: chain G residue 695 VAL Chi-restraints excluded: chain G residue 718 MET Chi-restraints excluded: chain G residue 719 THR Chi-restraints excluded: chain G residue 752 PHE Chi-restraints excluded: chain G residue 760 LEU Chi-restraints excluded: chain G residue 763 ILE Chi-restraints excluded: chain G residue 796 LEU Chi-restraints excluded: chain G residue 807 LEU Chi-restraints excluded: chain G residue 824 ILE Chi-restraints excluded: chain G residue 837 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 46 optimal weight: 7.9990 chunk 94 optimal weight: 30.0000 chunk 264 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 372 optimal weight: 0.7980 chunk 138 optimal weight: 20.0000 chunk 235 optimal weight: 5.9990 chunk 382 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 397 optimal weight: 4.9990 chunk 358 optimal weight: 0.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.137399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.109474 restraints weight = 59975.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.108994 restraints weight = 89248.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.109728 restraints weight = 90254.115| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 32487 Z= 0.190 Angle : 0.746 12.712 43932 Z= 0.345 Chirality : 0.045 0.312 5061 Planarity : 0.005 0.063 5705 Dihedral : 6.733 96.275 4608 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.66 % Favored : 93.16 % Rotamer: Outliers : 6.03 % Allowed : 27.80 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.14), residues: 3934 helix: 0.59 (0.12), residues: 1988 sheet: -0.14 (0.21), residues: 637 loop : -1.02 (0.20), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 823 HIS 0.023 0.001 HIS A 388 PHE 0.015 0.002 PHE A 625 TYR 0.012 0.001 TYR C 655 ARG 0.012 0.000 ARG C 323 Details of bonding type rmsd hydrogen bonds : bond 0.04721 ( 1405) hydrogen bonds : angle 4.47540 ( 3963) covalent geometry : bond 0.00451 (32487) covalent geometry : angle 0.74597 (43932) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7868 Ramachandran restraints generated. 3934 Oldfield, 0 Emsley, 3934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7868 Ramachandran restraints generated. 3934 Oldfield, 0 Emsley, 3934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 295 time to evaluate : 4.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LYS cc_start: 0.7510 (pttm) cc_final: 0.7054 (tmmt) REVERT: A 325 TYR cc_start: 0.7256 (m-10) cc_final: 0.7029 (m-10) REVERT: A 544 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7214 (ppt170) REVERT: A 625 PHE cc_start: 0.7529 (OUTLIER) cc_final: 0.6691 (p90) REVERT: A 692 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.7407 (tt) REVERT: A 771 HIS cc_start: 0.6905 (OUTLIER) cc_final: 0.6281 (m-70) REVERT: B 544 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7946 (ppt170) REVERT: B 752 PHE cc_start: 0.6886 (OUTLIER) cc_final: 0.6293 (m-80) REVERT: B 771 HIS cc_start: 0.7002 (OUTLIER) cc_final: 0.6413 (m-70) REVERT: C 752 PHE cc_start: 0.6677 (OUTLIER) cc_final: 0.6340 (m-80) REVERT: C 760 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8410 (mm) REVERT: C 771 HIS cc_start: 0.6803 (OUTLIER) cc_final: 0.6056 (m-70) REVERT: C 782 MET cc_start: 0.8616 (tpp) cc_final: 0.8207 (tpp) REVERT: D 598 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7846 (mt0) REVERT: D 640 MET cc_start: 0.7437 (mmm) cc_final: 0.7193 (tpt) REVERT: D 752 PHE cc_start: 0.7005 (OUTLIER) cc_final: 0.6475 (m-80) REVERT: D 771 HIS cc_start: 0.7124 (OUTLIER) cc_final: 0.6516 (m-70) REVERT: E 752 PHE cc_start: 0.6676 (OUTLIER) cc_final: 0.5698 (m-80) REVERT: E 771 HIS cc_start: 0.6858 (OUTLIER) cc_final: 0.6382 (m-70) REVERT: F 600 THR cc_start: 0.8944 (p) cc_final: 0.8729 (p) REVERT: F 697 ASP cc_start: 0.6498 (t70) cc_final: 0.6227 (t70) REVERT: F 771 HIS cc_start: 0.7011 (OUTLIER) cc_final: 0.6448 (m-70) REVERT: G 323 ARG cc_start: 0.8374 (tmt170) cc_final: 0.8125 (tmm-80) REVERT: G 544 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7749 (ppt170) REVERT: G 752 PHE cc_start: 0.6688 (OUTLIER) cc_final: 0.5501 (m-80) outliers start: 204 outliers final: 168 residues processed: 465 average time/residue: 0.3865 time to fit residues: 302.0683 Evaluate side-chains 471 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 285 time to evaluate : 3.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 625 PHE Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 771 HIS Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 401 CYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 544 ARG Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 614 THR Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 771 HIS Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 401 CYS Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 695 VAL Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 718 MET Chi-restraints excluded: chain C residue 752 PHE Chi-restraints excluded: chain C residue 757 LEU Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 763 ILE Chi-restraints excluded: chain C residue 771 HIS Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 824 ILE Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 332 PHE Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 401 CYS Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 598 GLN Chi-restraints excluded: chain D residue 614 THR Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 752 PHE Chi-restraints excluded: chain D residue 757 LEU Chi-restraints excluded: chain D residue 763 ILE Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 771 HIS Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 824 ILE Chi-restraints excluded: chain D residue 847 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 401 CYS Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 556 ASN Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain E residue 620 LEU Chi-restraints excluded: chain E residue 692 LEU Chi-restraints excluded: chain E residue 695 VAL Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 752 PHE Chi-restraints excluded: chain E residue 757 LEU Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 765 ILE Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain E residue 771 HIS Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain E residue 837 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain F residue 401 CYS Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain F residue 556 ASN Chi-restraints excluded: chain F residue 557 ASP Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 696 LEU Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 720 SER Chi-restraints excluded: chain F residue 763 ILE Chi-restraints excluded: chain F residue 769 LEU Chi-restraints excluded: chain F residue 771 HIS Chi-restraints excluded: chain F residue 796 LEU Chi-restraints excluded: chain F residue 807 LEU Chi-restraints excluded: chain F residue 824 ILE Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain G residue 401 CYS Chi-restraints excluded: chain G residue 541 VAL Chi-restraints excluded: chain G residue 544 ARG Chi-restraints excluded: chain G residue 556 ASN Chi-restraints excluded: chain G residue 614 THR Chi-restraints excluded: chain G residue 692 LEU Chi-restraints excluded: chain G residue 695 VAL Chi-restraints excluded: chain G residue 718 MET Chi-restraints excluded: chain G residue 719 THR Chi-restraints excluded: chain G residue 752 PHE Chi-restraints excluded: chain G residue 760 LEU Chi-restraints excluded: chain G residue 763 ILE Chi-restraints excluded: chain G residue 796 LEU Chi-restraints excluded: chain G residue 807 LEU Chi-restraints excluded: chain G residue 824 ILE Chi-restraints excluded: chain G residue 837 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 0 optimal weight: 20.0000 chunk 210 optimal weight: 3.9990 chunk 329 optimal weight: 8.9990 chunk 47 optimal weight: 0.0060 chunk 141 optimal weight: 1.9990 chunk 255 optimal weight: 4.9990 chunk 358 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 337 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 261 optimal weight: 0.6980 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 GLN D 378 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.140150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.111943 restraints weight = 59804.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110638 restraints weight = 77177.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.112117 restraints weight = 82827.014| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32487 Z= 0.120 Angle : 0.706 13.285 43932 Z= 0.319 Chirality : 0.043 0.337 5061 Planarity : 0.004 0.057 5705 Dihedral : 6.509 93.252 4608 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.30 % Favored : 93.52 % Rotamer: Outliers : 4.61 % Allowed : 29.34 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 3934 helix: 0.58 (0.12), residues: 1995 sheet: 0.01 (0.21), residues: 637 loop : -1.02 (0.20), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 823 HIS 0.005 0.001 HIS D 284 PHE 0.018 0.001 PHE G 625 TYR 0.012 0.001 TYR B 325 ARG 0.014 0.000 ARG C 323 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 1405) hydrogen bonds : angle 4.38005 ( 3963) covalent geometry : bond 0.00267 (32487) covalent geometry : angle 0.70600 (43932) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7868 Ramachandran restraints generated. 3934 Oldfield, 0 Emsley, 3934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7868 Ramachandran restraints generated. 3934 Oldfield, 0 Emsley, 3934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 295 time to evaluate : 3.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LYS cc_start: 0.7482 (pttm) cc_final: 0.7040 (tmmt) REVERT: A 325 TYR cc_start: 0.7273 (m-10) cc_final: 0.7007 (m-10) REVERT: A 544 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7130 (ppt170) REVERT: A 692 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.7494 (tt) REVERT: A 771 HIS cc_start: 0.6584 (OUTLIER) cc_final: 0.5979 (m-70) REVERT: B 428 GLU cc_start: 0.7870 (pt0) cc_final: 0.7535 (pt0) REVERT: B 544 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7897 (ppt170) REVERT: B 752 PHE cc_start: 0.6822 (OUTLIER) cc_final: 0.6283 (m-80) REVERT: B 771 HIS cc_start: 0.6873 (OUTLIER) cc_final: 0.6282 (m-70) REVERT: C 752 PHE cc_start: 0.6684 (OUTLIER) cc_final: 0.6211 (m-80) REVERT: C 760 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8311 (mm) REVERT: D 752 PHE cc_start: 0.6933 (OUTLIER) cc_final: 0.6364 (m-80) REVERT: D 771 HIS cc_start: 0.6853 (OUTLIER) cc_final: 0.6148 (m-70) REVERT: E 317 THR cc_start: 0.9241 (t) cc_final: 0.9028 (m) REVERT: E 614 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8744 (m) REVERT: E 771 HIS cc_start: 0.6841 (OUTLIER) cc_final: 0.6298 (m-70) REVERT: F 305 MET cc_start: 0.8098 (pmm) cc_final: 0.7830 (pmm) REVERT: F 692 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.7459 (tt) REVERT: F 697 ASP cc_start: 0.6445 (t70) cc_final: 0.6121 (t70) REVERT: F 771 HIS cc_start: 0.6611 (OUTLIER) cc_final: 0.6091 (m-70) REVERT: G 544 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7660 (ppt170) REVERT: G 692 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7806 (tp) REVERT: G 752 PHE cc_start: 0.6637 (OUTLIER) cc_final: 0.5562 (m-80) outliers start: 156 outliers final: 128 residues processed: 430 average time/residue: 0.3867 time to fit residues: 278.5290 Evaluate side-chains 429 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 284 time to evaluate : 3.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 771 HIS Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 544 ARG Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 614 THR Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain B residue 771 HIS Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 695 VAL Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 718 MET Chi-restraints excluded: chain C residue 752 PHE Chi-restraints excluded: chain C residue 757 LEU Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 824 ILE Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 752 PHE Chi-restraints excluded: chain D residue 763 ILE Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 771 HIS Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 824 ILE Chi-restraints excluded: chain E residue 179 LYS Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 401 CYS Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 556 ASN Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain E residue 620 LEU Chi-restraints excluded: chain E residue 692 LEU Chi-restraints excluded: chain E residue 695 VAL Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain E residue 757 LEU Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 765 ILE Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain E residue 771 HIS Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain E residue 837 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain F residue 556 ASN Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 696 LEU Chi-restraints excluded: chain F residue 720 SER Chi-restraints excluded: chain F residue 771 HIS Chi-restraints excluded: chain F residue 796 LEU Chi-restraints excluded: chain F residue 807 LEU Chi-restraints excluded: chain F residue 824 ILE Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain G residue 541 VAL Chi-restraints excluded: chain G residue 544 ARG Chi-restraints excluded: chain G residue 556 ASN Chi-restraints excluded: chain G residue 614 THR Chi-restraints excluded: chain G residue 692 LEU Chi-restraints excluded: chain G residue 695 VAL Chi-restraints excluded: chain G residue 752 PHE Chi-restraints excluded: chain G residue 760 LEU Chi-restraints excluded: chain G residue 796 LEU Chi-restraints excluded: chain G residue 807 LEU Chi-restraints excluded: chain G residue 824 ILE Chi-restraints excluded: chain G residue 837 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 21 optimal weight: 6.9990 chunk 347 optimal weight: 10.0000 chunk 311 optimal weight: 0.4980 chunk 60 optimal weight: 5.9990 chunk 351 optimal weight: 6.9990 chunk 382 optimal weight: 0.8980 chunk 189 optimal weight: 1.9990 chunk 310 optimal weight: 5.9990 chunk 369 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 185 optimal weight: 7.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.137733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.109045 restraints weight = 60029.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.108557 restraints weight = 81510.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.110159 restraints weight = 85214.001| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32487 Z= 0.181 Angle : 0.749 12.802 43932 Z= 0.345 Chirality : 0.045 0.324 5061 Planarity : 0.005 0.062 5705 Dihedral : 6.677 95.824 4608 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.81 % Favored : 93.01 % Rotamer: Outliers : 4.91 % Allowed : 29.19 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3934 helix: 0.57 (0.12), residues: 1988 sheet: -0.06 (0.21), residues: 637 loop : -1.01 (0.20), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 823 HIS 0.005 0.001 HIS F 388 PHE 0.018 0.001 PHE G 625 TYR 0.011 0.001 TYR B 325 ARG 0.012 0.000 ARG C 323 Details of bonding type rmsd hydrogen bonds : bond 0.04468 ( 1405) hydrogen bonds : angle 4.44214 ( 3963) covalent geometry : bond 0.00433 (32487) covalent geometry : angle 0.74925 (43932) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8920.02 seconds wall clock time: 161 minutes 6.68 seconds (9666.68 seconds total)