Starting phenix.real_space_refine on Tue Aug 26 00:16:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ip0_60751/08_2025/9ip0_60751.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ip0_60751/08_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_60751/08_2025/9ip0_60751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ip0_60751/08_2025/9ip0_60751.map" model { file = "/net/cci-nas-00/data/ceres_data/9ip0_60751/08_2025/9ip0_60751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ip0_60751/08_2025/9ip0_60751.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.031 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 8.11, per 1000 atoms: 0.25 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: 3.13 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 1.2 microseconds 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: 1.48 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: 6.85 Time building geometry restraints manager: 4.13 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: 0.02 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.970 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.950 ------------------------------------------------------------------------------- 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 : 8.32 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.014 0.000 ARG F 323 TYR 0.018 0.001 TYR C 325 PHE 0.019 0.001 PHE A 689 TRP 0.006 0.001 TRP B 823 HIS 0.014 0.001 HIS C 429 Details of bonding type rmsd covalent geometry : bond 0.00279 (32487) covalent geometry : angle 0.73368 (43932) hydrogen bonds : bond 0.15941 ( 1405) hydrogen bonds : angle 5.56458 ( 3963) *********************** 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 : 1.383 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: 0.1991 time to fit residues: 104.7422 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 : 1.288 ------------------------------------------------------------------------------- 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 197 optimal weight: 2.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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** E 310 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.140406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111183 restraints weight = 60942.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.109215 restraints weight = 75376.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110358 restraints weight = 74479.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.111444 restraints weight = 52230.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.112208 restraints weight = 45759.857| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.0725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32487 Z= 0.148 Angle : 0.665 9.023 43932 Z= 0.308 Chirality : 0.043 0.270 5061 Planarity : 0.005 0.058 5705 Dihedral : 6.462 92.318 4619 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.85 % Favored : 94.00 % Rotamer: Outliers : 3.61 % Allowed : 26.12 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.14), residues: 3934 helix: 0.80 (0.12), residues: 2002 sheet: 0.41 (0.23), residues: 532 loop : -1.18 (0.18), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 323 TYR 0.009 0.001 TYR C 322 PHE 0.022 0.001 PHE F 258 TRP 0.006 0.001 TRP B 823 HIS 0.006 0.001 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00346 (32487) covalent geometry : angle 0.66517 (43932) hydrogen bonds : bond 0.04303 ( 1405) hydrogen bonds : angle 4.67350 ( 3963) *********************** 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 456 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 334 time to evaluate : 1.117 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 556 ASN cc_start: 0.6599 (OUTLIER) cc_final: 0.6223 (p0) REVERT: B 323 ARG cc_start: 0.8240 (tmt170) cc_final: 0.7900 (ttp80) REVERT: B 665 THR cc_start: 0.8398 (p) cc_final: 0.8143 (t) REVERT: C 323 ARG cc_start: 0.8215 (tmt170) cc_final: 0.7614 (ttp80) REVERT: D 665 THR cc_start: 0.8445 (p) cc_final: 0.8162 (t) REVERT: D 752 PHE cc_start: 0.7150 (OUTLIER) cc_final: 0.6772 (m-80) REVERT: E 559 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8445 (pm20) REVERT: E 665 THR cc_start: 0.8538 (p) cc_final: 0.8284 (t) REVERT: E 752 PHE cc_start: 0.6824 (OUTLIER) cc_final: 0.6492 (m-10) REVERT: G 323 ARG cc_start: 0.8610 (tmt170) cc_final: 0.8104 (ttp80) REVERT: G 752 PHE cc_start: 0.6772 (OUTLIER) cc_final: 0.5650 (m-80) outliers start: 122 outliers final: 74 residues processed: 422 average time/residue: 0.1689 time to fit residues: 119.2198 Evaluate side-chains 377 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 298 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 602 SER 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 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 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 351 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 188 optimal weight: 0.0570 chunk 201 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 395 optimal weight: 5.9990 chunk 345 optimal weight: 6.9990 chunk 327 optimal weight: 9.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- 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 C 424 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 = 0.3832 r_free = 0.3832 target = 0.140043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.113425 restraints weight = 60037.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.113297 restraints weight = 82650.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.114147 restraints weight = 78142.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.114714 restraints weight = 54968.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.115184 restraints weight = 51922.715| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 32487 Z= 0.148 Angle : 0.665 10.546 43932 Z= 0.307 Chirality : 0.043 0.220 5061 Planarity : 0.004 0.061 5705 Dihedral : 6.463 92.465 4608 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.28 % Favored : 93.54 % Rotamer: Outliers : 4.70 % Allowed : 26.83 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.14), residues: 3934 helix: 0.78 (0.12), residues: 2002 sheet: 0.12 (0.25), residues: 441 loop : -1.09 (0.18), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 323 TYR 0.010 0.001 TYR F 655 PHE 0.011 0.001 PHE B 258 TRP 0.006 0.001 TRP C 823 HIS 0.004 0.001 HIS F 388 Details of bonding type rmsd covalent geometry : bond 0.00346 (32487) covalent geometry : angle 0.66481 (43932) hydrogen bonds : bond 0.04237 ( 1405) hydrogen bonds : angle 4.53705 ( 3963) *********************** 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 478 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 319 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 428 GLU cc_start: 0.7530 (pt0) cc_final: 0.7154 (pt0) REVERT: B 665 THR cc_start: 0.8255 (p) cc_final: 0.8053 (t) REVERT: D 665 THR cc_start: 0.8275 (p) cc_final: 0.8008 (t) REVERT: D 752 PHE cc_start: 0.7205 (OUTLIER) cc_final: 0.6735 (m-80) REVERT: E 189 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7964 (mm-30) REVERT: E 559 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8250 (pp20) REVERT: E 752 PHE cc_start: 0.6815 (OUTLIER) cc_final: 0.6367 (m-80) REVERT: F 692 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.7503 (tt) REVERT: F 697 ASP cc_start: 0.6475 (t70) cc_final: 0.6140 (t70) REVERT: G 544 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7633 (ppt170) REVERT: G 752 PHE cc_start: 0.6800 (OUTLIER) cc_final: 0.5721 (m-80) outliers start: 159 outliers final: 119 residues processed: 438 average time/residue: 0.1830 time to fit residues: 133.1897 Evaluate side-chains 409 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 283 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 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 384 ILE Chi-restraints excluded: chain A residue 541 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 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 796 LEU 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 310 GLN 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 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 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 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 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 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 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 189 GLU 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 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 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 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 645 VAL Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 757 LEU 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 241 ILE 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 718 MET 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 837 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 89 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 chunk 327 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 248 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 330 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 340 optimal weight: 0.3980 chunk 16 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 694 GLN ** G 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.141770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.115411 restraints weight = 59353.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.113131 restraints weight = 81616.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.114190 restraints weight = 84338.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.114978 restraints weight = 57157.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.115319 restraints weight = 53995.496| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 32487 Z= 0.110 Angle : 0.643 12.554 43932 Z= 0.292 Chirality : 0.042 0.241 5061 Planarity : 0.004 0.056 5705 Dihedral : 6.346 90.270 4608 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.54 % Favored : 94.28 % Rotamer: Outliers : 4.35 % Allowed : 27.21 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.14), residues: 3934 helix: 0.79 (0.12), residues: 2002 sheet: 0.28 (0.22), residues: 567 loop : -1.15 (0.19), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 323 TYR 0.007 0.001 TYR B 325 PHE 0.010 0.001 PHE D 258 TRP 0.005 0.001 TRP F 823 HIS 0.004 0.001 HIS E 388 Details of bonding type rmsd covalent geometry : bond 0.00242 (32487) covalent geometry : angle 0.64288 (43932) hydrogen bonds : bond 0.03565 ( 1405) hydrogen bonds : angle 4.43963 ( 3963) *********************** 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 470 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 323 time to evaluate : 0.914 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: B 323 ARG cc_start: 0.8348 (tmt170) cc_final: 0.7897 (ttp80) REVERT: B 428 GLU cc_start: 0.7867 (pt0) cc_final: 0.7397 (pt0) REVERT: B 665 THR cc_start: 0.8273 (p) cc_final: 0.8025 (t) REVERT: C 752 PHE cc_start: 0.6509 (OUTLIER) cc_final: 0.6272 (m-80) REVERT: D 665 THR cc_start: 0.8271 (p) cc_final: 0.7986 (t) REVERT: D 752 PHE cc_start: 0.7052 (OUTLIER) cc_final: 0.6618 (m-80) REVERT: E 559 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8180 (pp20) REVERT: E 752 PHE cc_start: 0.6782 (OUTLIER) cc_final: 0.6075 (m-80) REVERT: F 692 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.7457 (tt) REVERT: F 697 ASP cc_start: 0.6262 (t70) cc_final: 0.5923 (t70) REVERT: G 323 ARG cc_start: 0.8417 (tmt170) cc_final: 0.7908 (ttp80) REVERT: G 544 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7682 (ppt170) REVERT: G 692 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.7975 (tp) outliers start: 147 outliers final: 99 residues processed: 440 average time/residue: 0.1727 time to fit residues: 127.0147 Evaluate side-chains 402 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 296 time to evaluate : 1.352 ------------------------------------------------------------------------------- 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 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 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 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 541 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 695 VAL 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 248 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 695 VAL Chi-restraints excluded: chain C residue 715 VAL 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 796 LEU Chi-restraints excluded: chain C residue 824 ILE 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 384 ILE 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 715 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 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 556 ASN Chi-restraints excluded: chain E residue 559 GLU 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 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 384 ILE Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 541 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 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 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 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 722 LEU 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 395 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 58 optimal weight: 0.2980 chunk 371 optimal weight: 6.9990 chunk 179 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 375 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 169 optimal weight: 0.0770 chunk 177 optimal weight: 0.0570 chunk 343 optimal weight: 6.9990 overall best weight: 1.2860 ------------------------------------------------------------------------------- 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 = 0.3852 r_free = 0.3852 target = 0.141688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.116400 restraints weight = 59496.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.115332 restraints weight = 86894.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.116602 restraints weight = 84931.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.116753 restraints weight = 55011.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.117829 restraints weight = 51226.522| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 32487 Z= 0.114 Angle : 0.653 12.348 43932 Z= 0.296 Chirality : 0.043 0.293 5061 Planarity : 0.004 0.056 5705 Dihedral : 6.307 89.783 4608 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.02 % Favored : 93.80 % Rotamer: Outliers : 4.88 % Allowed : 27.24 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.14), residues: 3934 helix: 0.78 (0.12), residues: 2002 sheet: 0.28 (0.22), residues: 567 loop : -1.11 (0.19), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 323 TYR 0.009 0.001 TYR E 655 PHE 0.018 0.001 PHE D 258 TRP 0.005 0.001 TRP F 823 HIS 0.004 0.001 HIS F 388 Details of bonding type rmsd covalent geometry : bond 0.00258 (32487) covalent geometry : angle 0.65259 (43932) hydrogen bonds : bond 0.03506 ( 1405) hydrogen bonds : angle 4.39482 ( 3963) *********************** 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 481 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 316 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 717 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8610 (mt) REVERT: B 323 ARG cc_start: 0.8259 (tmt170) cc_final: 0.7925 (ttp80) REVERT: B 428 GLU cc_start: 0.7771 (pt0) cc_final: 0.7304 (pt0) REVERT: B 544 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7825 (ppt170) REVERT: B 665 THR cc_start: 0.8304 (p) cc_final: 0.8043 (t) REVERT: C 752 PHE cc_start: 0.6694 (OUTLIER) cc_final: 0.6458 (m-10) REVERT: C 760 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8314 (mm) REVERT: D 321 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6950 (mm-30) REVERT: D 665 THR cc_start: 0.8316 (p) cc_final: 0.8026 (t) REVERT: D 752 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.6490 (m-80) REVERT: E 559 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8222 (pp20) REVERT: E 614 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8780 (m) REVERT: E 752 PHE cc_start: 0.6778 (OUTLIER) cc_final: 0.5830 (m-80) REVERT: F 692 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.7456 (tt) REVERT: F 697 ASP cc_start: 0.6255 (t70) cc_final: 0.5926 (t70) REVERT: G 323 ARG cc_start: 0.8269 (tmt170) cc_final: 0.8007 (ttp80) REVERT: G 544 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7767 (ppt170) REVERT: G 692 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.7977 (tp) REVERT: G 752 PHE cc_start: 0.6667 (OUTLIER) cc_final: 0.5509 (m-80) outliers start: 165 outliers final: 126 residues processed: 449 average time/residue: 0.1676 time to fit residues: 127.1205 Evaluate side-chains 437 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 299 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 384 ILE 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 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 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 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 717 ILE Chi-restraints excluded: chain B residue 719 THR 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 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 248 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 401 CYS 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 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 769 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 824 ILE Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 286 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 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 719 THR Chi-restraints excluded: chain D residue 752 PHE 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 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 541 VAL Chi-restraints excluded: chain E residue 559 GLU 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 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 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 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 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 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 56 optimal weight: 8.9990 chunk 269 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 229 optimal weight: 0.4980 chunk 20 optimal weight: 0.0870 chunk 239 optimal weight: 10.0000 chunk 187 optimal weight: 5.9990 chunk 309 optimal weight: 9.9990 chunk 219 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 overall best weight: 1.1960 ------------------------------------------------------------------------------- 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 = 0.3852 r_free = 0.3852 target = 0.141711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.113906 restraints weight = 59439.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.112003 restraints weight = 75951.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.113069 restraints weight = 78980.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.114308 restraints weight = 52549.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.114666 restraints weight = 46085.134| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 32487 Z= 0.112 Angle : 0.650 9.804 43932 Z= 0.293 Chirality : 0.042 0.304 5061 Planarity : 0.004 0.056 5705 Dihedral : 6.228 89.232 4606 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.69 % Favored : 94.13 % Rotamer: Outliers : 5.15 % Allowed : 27.36 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.14), residues: 3934 helix: 0.77 (0.12), residues: 1995 sheet: 0.15 (0.25), residues: 441 loop : -0.94 (0.18), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 323 TYR 0.007 0.001 TYR G 325 PHE 0.010 0.001 PHE D 258 TRP 0.004 0.001 TRP F 823 HIS 0.004 0.001 HIS F 388 Details of bonding type rmsd covalent geometry : bond 0.00252 (32487) covalent geometry : angle 0.65030 (43932) hydrogen bonds : bond 0.03375 ( 1405) hydrogen bonds : angle 4.33774 ( 3963) *********************** 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 497 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 323 time to evaluate : 0.809 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 692 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.7426 (tt) REVERT: A 717 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8719 (mt) REVERT: B 428 GLU cc_start: 0.8021 (pt0) cc_final: 0.7525 (pt0) REVERT: B 544 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7800 (ppt170) REVERT: B 665 THR cc_start: 0.8328 (p) cc_final: 0.8060 (t) REVERT: B 752 PHE cc_start: 0.6791 (OUTLIER) cc_final: 0.6199 (m-80) REVERT: C 752 PHE cc_start: 0.6724 (OUTLIER) cc_final: 0.6481 (m-10) REVERT: C 760 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8275 (mm) REVERT: D 321 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7049 (mm-30) REVERT: D 598 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7836 (mt0) REVERT: D 665 THR cc_start: 0.8431 (p) cc_final: 0.8138 (t) REVERT: D 719 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8409 (p) REVERT: D 752 PHE cc_start: 0.6919 (OUTLIER) cc_final: 0.6399 (m-80) REVERT: E 189 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7914 (mm-30) REVERT: E 559 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8304 (pp20) REVERT: E 614 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8774 (m) REVERT: F 317 THR cc_start: 0.8849 (t) cc_final: 0.8642 (m) REVERT: F 692 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.7436 (tt) REVERT: F 697 ASP cc_start: 0.6350 (t70) cc_final: 0.6059 (t70) REVERT: G 544 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7706 (ppt170) REVERT: G 692 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7901 (tp) REVERT: G 752 PHE cc_start: 0.6747 (OUTLIER) cc_final: 0.5632 (m-80) outliers start: 174 outliers final: 140 residues processed: 464 average time/residue: 0.1632 time to fit residues: 128.6730 Evaluate side-chains 461 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 305 time to evaluate : 1.339 ------------------------------------------------------------------------------- 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 318 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 384 ILE 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 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 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 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 384 ILE 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 697 ASP 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 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 248 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 401 CYS 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 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 769 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 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 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 796 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 824 ILE Chi-restraints excluded: chain E residue 189 GLU 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 559 GLU 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 709 VAL Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain E residue 722 LEU 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 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 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 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 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 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 306 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 297 optimal weight: 0.7980 chunk 307 optimal weight: 3.9990 chunk 360 optimal weight: 0.6980 chunk 251 optimal weight: 8.9990 chunk 295 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 234 optimal weight: 0.5980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 310 GLN ** G 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.142317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.114811 restraints weight = 59622.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.114110 restraints weight = 72192.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.115539 restraints weight = 72871.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.115664 restraints weight = 46773.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.116380 restraints weight = 44288.245| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1357 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= 0.113 Angle : 0.664 11.239 43932 Z= 0.298 Chirality : 0.042 0.253 5061 Planarity : 0.004 0.056 5705 Dihedral : 6.187 88.771 4606 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.77 % Favored : 94.05 % Rotamer: Outliers : 5.59 % Allowed : 27.33 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.14), residues: 3934 helix: 0.73 (0.12), residues: 2002 sheet: 0.36 (0.22), residues: 567 loop : -1.07 (0.19), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 323 TYR 0.009 0.001 TYR E 655 PHE 0.008 0.001 PHE A 625 TRP 0.004 0.001 TRP C 823 HIS 0.012 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00256 (32487) covalent geometry : angle 0.66376 (43932) hydrogen bonds : bond 0.03307 ( 1405) hydrogen bonds : angle 4.31612 ( 3963) *********************** 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 509 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 320 time to evaluate : 1.170 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: 0.7579 (pttm) cc_final: 0.7227 (tmmt) REVERT: A 692 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.7501 (tt) REVERT: A 717 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8695 (mt) REVERT: B 428 GLU cc_start: 0.7990 (pt0) cc_final: 0.7699 (pt0) REVERT: B 544 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7846 (ppt170) REVERT: B 665 THR cc_start: 0.8342 (p) cc_final: 0.8075 (t) REVERT: B 752 PHE cc_start: 0.6814 (OUTLIER) cc_final: 0.6239 (m-80) REVERT: C 310 GLN cc_start: 0.2943 (OUTLIER) cc_final: 0.2719 (pm20) REVERT: C 717 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8714 (mt) REVERT: C 752 PHE cc_start: 0.6723 (OUTLIER) cc_final: 0.6403 (m-10) REVERT: C 760 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8245 (mm) REVERT: D 598 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7732 (mt0) REVERT: D 665 THR cc_start: 0.8387 (p) cc_final: 0.8092 (t) REVERT: D 752 PHE cc_start: 0.6917 (OUTLIER) cc_final: 0.6373 (m-80) REVERT: E 189 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7894 (mm-30) REVERT: E 317 THR cc_start: 0.9204 (t) cc_final: 0.8983 (m) REVERT: E 559 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8300 (pp20) REVERT: E 614 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8752 (m) REVERT: E 692 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.7377 (tt) REVERT: E 752 PHE cc_start: 0.6720 (OUTLIER) cc_final: 0.5727 (m-80) REVERT: F 317 THR cc_start: 0.8741 (t) cc_final: 0.8533 (m) REVERT: F 692 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.7469 (tt) REVERT: F 697 ASP cc_start: 0.6299 (t70) cc_final: 0.5998 (t70) REVERT: G 323 ARG cc_start: 0.8422 (tmt170) cc_final: 0.7827 (ttp80) REVERT: G 544 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7718 (ppt170) REVERT: G 692 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7904 (tp) REVERT: G 737 MET cc_start: 0.7387 (pmm) cc_final: 0.7160 (pmm) REVERT: G 752 PHE cc_start: 0.6713 (OUTLIER) cc_final: 0.5596 (m-80) outliers start: 189 outliers final: 145 residues processed: 474 average time/residue: 0.1671 time to fit residues: 133.2084 Evaluate side-chains 465 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 301 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 796 LEU Chi-restraints excluded: chain B residue 180 LEU 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 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 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 760 LEU Chi-restraints excluded: chain B residue 763 ILE 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 248 LEU Chi-restraints excluded: chain C residue 310 GLN Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 401 CYS 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 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 765 ILE Chi-restraints excluded: chain C residue 769 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 248 LEU 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 394 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 709 VAL Chi-restraints excluded: chain D residue 715 VAL 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 796 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 824 ILE Chi-restraints excluded: chain E residue 189 GLU 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 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 541 VAL Chi-restraints excluded: chain E residue 556 ASN Chi-restraints excluded: chain E residue 559 GLU 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 709 VAL 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 765 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 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 625 PHE 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 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 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 645 VAL 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 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 200 optimal weight: 1.9990 chunk 388 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 175 optimal weight: 0.9980 chunk 152 optimal weight: 0.0050 chunk 268 optimal weight: 8.9990 chunk 375 optimal weight: 0.8980 chunk 204 optimal weight: 0.9980 chunk 387 optimal weight: 0.9990 chunk 395 optimal weight: 3.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 GLN C 310 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 = 0.3864 r_free = 0.3864 target = 0.142620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.115033 restraints weight = 59528.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.113944 restraints weight = 73015.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.115490 restraints weight = 72782.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.115335 restraints weight = 48709.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.115733 restraints weight = 46794.685| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 32487 Z= 0.109 Angle : 0.677 13.275 43932 Z= 0.302 Chirality : 0.042 0.308 5061 Planarity : 0.004 0.054 5705 Dihedral : 6.120 87.463 4606 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.57 % Favored : 94.26 % Rotamer: Outliers : 5.03 % Allowed : 28.22 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.14), residues: 3934 helix: 0.69 (0.12), residues: 2023 sheet: 0.43 (0.22), residues: 567 loop : -1.02 (0.19), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 323 TYR 0.008 0.001 TYR D 325 PHE 0.009 0.001 PHE B 258 TRP 0.004 0.001 TRP F 823 HIS 0.008 0.001 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00241 (32487) covalent geometry : angle 0.67714 (43932) hydrogen bonds : bond 0.03096 ( 1405) hydrogen bonds : angle 4.30592 ( 3963) *********************** 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 495 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 325 time to evaluate : 1.279 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 179 LYS cc_start: 0.7441 (pttm) cc_final: 0.7123 (tmmt) REVERT: A 692 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.7504 (tt) REVERT: A 717 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8746 (mt) REVERT: B 428 GLU cc_start: 0.7996 (pt0) cc_final: 0.7530 (pt0) REVERT: B 544 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7806 (ppt170) REVERT: B 665 THR cc_start: 0.8304 (p) cc_final: 0.8047 (t) REVERT: B 752 PHE cc_start: 0.6814 (OUTLIER) cc_final: 0.6311 (m-80) REVERT: B 850 ASP cc_start: 0.8236 (m-30) cc_final: 0.7931 (p0) REVERT: C 717 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8760 (mt) REVERT: C 752 PHE cc_start: 0.6988 (OUTLIER) cc_final: 0.6623 (m-10) REVERT: C 760 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8189 (mm) REVERT: D 665 THR cc_start: 0.8323 (p) cc_final: 0.8010 (t) REVERT: E 559 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8283 (pp20) REVERT: E 614 THR cc_start: 0.8978 (OUTLIER) cc_final: 0.8754 (m) REVERT: E 692 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.7468 (tt) REVERT: E 752 PHE cc_start: 0.6691 (OUTLIER) cc_final: 0.5749 (m-80) REVERT: F 692 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.7482 (tt) REVERT: F 697 ASP cc_start: 0.6277 (t70) cc_final: 0.5973 (t70) REVERT: G 323 ARG cc_start: 0.8310 (tmt170) cc_final: 0.7797 (ttp80) REVERT: G 544 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7682 (ppt170) REVERT: G 692 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7955 (tp) REVERT: G 737 MET cc_start: 0.7348 (pmm) cc_final: 0.7134 (pmm) REVERT: G 752 PHE cc_start: 0.6718 (OUTLIER) cc_final: 0.5625 (m-80) outliers start: 170 outliers final: 136 residues processed: 464 average time/residue: 0.1702 time to fit residues: 134.5810 Evaluate side-chains 460 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 309 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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 384 ILE 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 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 715 VAL Chi-restraints excluded: chain A residue 717 ILE 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 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 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 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 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 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 310 GLN Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 541 VAL 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 765 ILE Chi-restraints excluded: chain C residue 769 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 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 394 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 625 PHE Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 709 VAL 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 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 559 GLU 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 719 THR Chi-restraints excluded: chain E residue 752 PHE Chi-restraints excluded: chain E residue 757 LEU Chi-restraints excluded: chain E residue 765 ILE Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain E residue 837 ILE 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 544 ARG Chi-restraints excluded: chain F residue 556 ASN Chi-restraints excluded: chain F residue 625 PHE 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 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 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 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 625 PHE Chi-restraints excluded: chain G residue 645 VAL 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 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 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 124 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 158 optimal weight: 6.9990 chunk 364 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 264 optimal weight: 8.9990 chunk 266 optimal weight: 8.9990 chunk 391 optimal weight: 4.9990 chunk 303 optimal weight: 4.9990 chunk 314 optimal weight: 3.9990 chunk 274 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 694 GLN E 338 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 = 0.3806 r_free = 0.3806 target = 0.137990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.109286 restraints weight = 60394.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.108652 restraints weight = 82695.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.109638 restraints weight = 82775.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110780 restraints weight = 54274.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.111196 restraints weight = 48038.864| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 32487 Z= 0.189 Angle : 0.756 12.395 43932 Z= 0.349 Chirality : 0.045 0.301 5061 Planarity : 0.005 0.062 5705 Dihedral : 6.527 94.112 4606 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.53 % Favored : 93.29 % Rotamer: Outliers : 5.32 % Allowed : 27.92 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.14), residues: 3934 helix: 0.70 (0.12), residues: 1995 sheet: -0.04 (0.21), residues: 637 loop : -0.95 (0.20), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 312 TYR 0.013 0.001 TYR D 322 PHE 0.012 0.002 PHE F 766 TRP 0.008 0.001 TRP C 823 HIS 0.020 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00451 (32487) covalent geometry : angle 0.75648 (43932) hydrogen bonds : bond 0.04646 ( 1405) hydrogen bonds : angle 4.39925 ( 3963) *********************** 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 481 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 301 time to evaluate : 1.188 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 692 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.7397 (tt) REVERT: B 428 GLU cc_start: 0.7955 (pt0) cc_final: 0.7570 (pt0) REVERT: B 544 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7938 (ppt170) REVERT: B 665 THR cc_start: 0.8378 (p) cc_final: 0.8162 (t) REVERT: B 752 PHE cc_start: 0.6892 (OUTLIER) cc_final: 0.6357 (m-80) REVERT: C 752 PHE cc_start: 0.6775 (OUTLIER) cc_final: 0.6469 (m-10) REVERT: C 760 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8381 (mm) REVERT: C 782 MET cc_start: 0.8603 (tpp) cc_final: 0.8204 (tpp) REVERT: D 752 PHE cc_start: 0.6967 (OUTLIER) cc_final: 0.6390 (m-80) REVERT: E 752 PHE cc_start: 0.6817 (OUTLIER) cc_final: 0.5832 (m-80) REVERT: F 692 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.7489 (tt) REVERT: F 697 ASP cc_start: 0.6446 (t70) cc_final: 0.6146 (t70) REVERT: G 323 ARG cc_start: 0.8392 (tmt170) cc_final: 0.7860 (ttp80) REVERT: G 325 TYR cc_start: 0.7209 (m-10) cc_final: 0.6997 (m-10) REVERT: G 385 MET cc_start: 0.7666 (tpp) cc_final: 0.7452 (tpp) REVERT: G 544 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7703 (ppt170) REVERT: G 737 MET cc_start: 0.7459 (pmm) cc_final: 0.7217 (pmm) REVERT: G 752 PHE cc_start: 0.6683 (OUTLIER) cc_final: 0.5485 (m-80) outliers start: 180 outliers final: 148 residues processed: 447 average time/residue: 0.1643 time to fit residues: 123.2890 Evaluate side-chains 442 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 284 time to evaluate : 1.690 ------------------------------------------------------------------------------- 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 208 ILE 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 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 692 LEU Chi-restraints excluded: chain A residue 695 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 796 LEU Chi-restraints excluded: chain B residue 180 LEU 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 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 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 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 356 LEU 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 769 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 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 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 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 719 THR 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 356 LEU Chi-restraints excluded: chain F residue 384 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 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 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 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 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 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 352 optimal weight: 6.9990 chunk 224 optimal weight: 0.6980 chunk 215 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 326 optimal weight: 4.9990 chunk 332 optimal weight: 0.9990 chunk 354 optimal weight: 0.0020 chunk 229 optimal weight: 30.0000 chunk 189 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 429 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.140701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.112529 restraints weight = 59613.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.111922 restraints weight = 80381.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.113319 restraints weight = 82583.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.113516 restraints weight = 54614.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.114163 restraints weight = 49874.331| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32487 Z= 0.123 Angle : 0.715 13.383 43932 Z= 0.322 Chirality : 0.043 0.324 5061 Planarity : 0.004 0.056 5705 Dihedral : 6.343 91.257 4606 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.87 % Favored : 93.95 % Rotamer: Outliers : 4.32 % Allowed : 29.04 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.14), residues: 3934 helix: 0.69 (0.12), residues: 1995 sheet: 0.06 (0.21), residues: 637 loop : -0.99 (0.19), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 323 TYR 0.012 0.001 TYR E 322 PHE 0.018 0.001 PHE A 625 TRP 0.005 0.001 TRP C 823 HIS 0.008 0.001 HIS E 284 Details of bonding type rmsd covalent geometry : bond 0.00281 (32487) covalent geometry : angle 0.71459 (43932) hydrogen bonds : bond 0.03643 ( 1405) hydrogen bonds : angle 4.33756 ( 3963) ********************** 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 449 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 303 time to evaluate : 0.950 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: 0.7552 (pttm) cc_final: 0.7152 (tmmt) REVERT: A 385 MET cc_start: 0.7464 (tpp) cc_final: 0.7163 (tpt) REVERT: A 692 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.7469 (tt) REVERT: B 428 GLU cc_start: 0.8108 (pt0) cc_final: 0.7592 (pt0) REVERT: B 544 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7877 (ppt170) REVERT: B 665 THR cc_start: 0.8353 (p) cc_final: 0.8145 (t) REVERT: B 752 PHE cc_start: 0.6825 (OUTLIER) cc_final: 0.6306 (m-80) REVERT: C 752 PHE cc_start: 0.6753 (OUTLIER) cc_final: 0.6378 (m-10) REVERT: C 760 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8262 (mm) REVERT: D 752 PHE cc_start: 0.6891 (OUTLIER) cc_final: 0.6236 (m-80) REVERT: E 614 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8708 (m) REVERT: E 692 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.7586 (tt) REVERT: E 752 PHE cc_start: 0.6732 (OUTLIER) cc_final: 0.5786 (m-80) REVERT: F 692 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.7452 (tt) REVERT: F 697 ASP cc_start: 0.6354 (t70) cc_final: 0.6056 (t70) REVERT: G 323 ARG cc_start: 0.8348 (tmt170) cc_final: 0.7802 (ttp80) REVERT: G 385 MET cc_start: 0.7758 (tpp) cc_final: 0.7491 (tpp) REVERT: G 544 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7677 (ppt170) REVERT: G 692 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7768 (tp) REVERT: G 737 MET cc_start: 0.7344 (pmm) cc_final: 0.7130 (pmm) REVERT: G 752 PHE cc_start: 0.6652 (OUTLIER) cc_final: 0.5544 (m-80) outliers start: 146 outliers final: 127 residues processed: 424 average time/residue: 0.1721 time to fit residues: 123.2515 Evaluate side-chains 431 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 291 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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 384 ILE 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 692 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 717 ILE 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 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 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 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 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 302 PHE 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 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 769 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 541 VAL Chi-restraints excluded: chain D residue 556 ASN 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 204 ASN Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 ILE 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 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 193 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 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 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 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 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 126 optimal weight: 0.3980 chunk 137 optimal weight: 0.0070 chunk 215 optimal weight: 5.9990 chunk 327 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 240 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 284 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 374 optimal weight: 0.9990 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 429 HIS G 663 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.141799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.113440 restraints weight = 59957.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.112097 restraints weight = 80054.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.113218 restraints weight = 81295.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.114668 restraints weight = 54241.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.114902 restraints weight = 48057.685| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32487 Z= 0.114 Angle : 0.706 13.492 43932 Z= 0.317 Chirality : 0.043 0.327 5061 Planarity : 0.004 0.053 5705 Dihedral : 6.197 89.107 4606 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.80 % Favored : 94.03 % Rotamer: Outliers : 4.14 % Allowed : 29.31 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.14), residues: 3934 helix: 0.71 (0.12), residues: 2002 sheet: -0.03 (0.24), residues: 511 loop : -0.83 (0.19), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 422 TYR 0.012 0.001 TYR C 325 PHE 0.017 0.001 PHE A 625 TRP 0.005 0.001 TRP B 823 HIS 0.005 0.001 HIS E 284 Details of bonding type rmsd covalent geometry : bond 0.00254 (32487) covalent geometry : angle 0.70560 (43932) hydrogen bonds : bond 0.03134 ( 1405) hydrogen bonds : angle 4.29904 ( 3963) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3974.43 seconds wall clock time: 69 minutes 43.59 seconds (4183.59 seconds total)