Starting phenix.real_space_refine on Tue Sep 15 06:23:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6aui_7006/09_2026/6aui_7006.cif Found real_map, /net/cci-nas-00/data/ceres_data/6aui_7006/09_2026/6aui_7006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6aui_7006/09_2026/6aui_7006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6aui_7006/09_2026/6aui_7006.map" model { file = "/net/cci-nas-00/data/ceres_data/6aui_7006/09_2026/6aui_7006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6aui_7006/09_2026/6aui_7006.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6aui_7006/09_2026/6aui_7006.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6aui_7006/09_2026/6aui_7006.cif" } resolution = 3.3 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 48 5.49 5 Mg 12 5.21 5 S 204 5.16 5 C 22938 2.51 5 N 6150 2.21 5 O 6954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.16s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36306 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5958 Classifications: {'peptide': 745} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 715} Chain: "B" Number of atoms: 5958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5958 Classifications: {'peptide': 745} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 715} Chain: "C" Number of atoms: 5958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5958 Classifications: {'peptide': 745} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 715} Chain: "D" Number of atoms: 5958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5958 Classifications: {'peptide': 745} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 715} Chain: "E" Number of atoms: 5958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5958 Classifications: {'peptide': 745} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 715} Chain: "F" Number of atoms: 5958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5958 Classifications: {'peptide': 745} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 715} Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {' MG': 2, 'CDP': 1, 'DTP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {' MG': 2, 'CDP': 1, 'DTP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {' MG': 2, 'CDP': 1, 'DTP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {' MG': 2, 'CDP': 1, 'DTP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {' MG': 2, 'CDP': 1, 'DTP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {' MG': 2, 'CDP': 1, 'DTP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 7.14, per 1000 atoms: 0.20 Number of scatterers: 36306 At special positions: 0 Unit cell: (178.16, 195.19, 116.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 204 16.00 P 48 15.00 Mg 12 11.99 O 6954 8.00 N 6150 7.00 C 22938 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: 3.30 Conformation dependent library (CDL) restraints added in 1.1 seconds 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8424 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 48 sheets defined 54.6% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 15 through 23 removed outlier: 3.883A pdb=" N THR A 19 " --> pdb=" O PHE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 27 removed outlier: 4.272A pdb=" N TYR A 27 " --> pdb=" O LYS A 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 24 through 27' Processing helix chain 'A' and resid 35 through 47 removed outlier: 4.017A pdb=" N ILE A 39 " --> pdb=" O ASP A 35 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 68 removed outlier: 3.751A pdb=" N LEU A 56 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 72 through 90 removed outlier: 4.265A pdb=" N ILE A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 103 removed outlier: 3.614A pdb=" N VAL A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 127 through 135 removed outlier: 3.603A pdb=" N SER A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 143 removed outlier: 3.731A pdb=" N ARG A 139 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP A 140 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE A 141 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR A 143 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 155 removed outlier: 3.940A pdb=" N SER A 154 " --> pdb=" O THR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 179 Processing helix chain 'A' and resid 183 through 195 Processing helix chain 'A' and resid 201 through 207 Processing helix chain 'A' and resid 227 through 244 Processing helix chain 'A' and resid 272 through 286 Processing helix chain 'A' and resid 307 through 313 Processing helix chain 'A' and resid 320 through 324 Processing helix chain 'A' and resid 335 through 344 removed outlier: 3.965A pdb=" N MET A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 377 Processing helix chain 'A' and resid 386 through 400 Processing helix chain 'A' and resid 408 through 414 Processing helix chain 'A' and resid 463 through 482 removed outlier: 3.517A pdb=" N ALA A 467 " --> pdb=" O PHE A 463 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASP A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 498 removed outlier: 4.237A pdb=" N CYS A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU A 493 " --> pdb=" O PRO A 489 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 515 removed outlier: 3.776A pdb=" N ALA A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 551 removed outlier: 3.971A pdb=" N GLN A 525 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A 529 " --> pdb=" O GLN A 525 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A 549 " --> pdb=" O ASP A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 571 removed outlier: 3.668A pdb=" N MET A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 592 removed outlier: 4.080A pdb=" N LEU A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 612 removed outlier: 3.556A pdb=" N ALA A 608 " --> pdb=" O THR A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 649 removed outlier: 3.674A pdb=" N GLU A 647 " --> pdb=" O LYS A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 661 removed outlier: 4.060A pdb=" N ALA A 661 " --> pdb=" O ASN A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 669 removed outlier: 3.846A pdb=" N SER A 668 " --> pdb=" O SER A 665 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 669 " --> pdb=" O ILE A 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 669' Processing helix chain 'A' and resid 675 through 680 Processing helix chain 'A' and resid 682 through 686 Processing helix chain 'A' and resid 687 through 701 removed outlier: 3.940A pdb=" N VAL A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 731 Processing helix chain 'B' and resid 15 through 23 removed outlier: 3.884A pdb=" N THR B 19 " --> pdb=" O PHE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 27 removed outlier: 4.271A pdb=" N TYR B 27 " --> pdb=" O LYS B 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 24 through 27' Processing helix chain 'B' and resid 35 through 47 removed outlier: 4.017A pdb=" N ILE B 39 " --> pdb=" O ASP B 35 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 68 removed outlier: 3.751A pdb=" N LEU B 56 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 72 through 90 removed outlier: 4.266A pdb=" N ILE B 76 " --> pdb=" O PRO B 72 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 89 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 103 removed outlier: 3.615A pdb=" N VAL B 97 " --> pdb=" O VAL B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 127 Processing helix chain 'B' and resid 127 through 135 removed outlier: 3.603A pdb=" N SER B 133 " --> pdb=" O ASP B 129 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 143 removed outlier: 3.731A pdb=" N ARG B 139 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP B 140 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE B 141 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR B 143 " --> pdb=" O ASP B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 155 removed outlier: 3.940A pdb=" N SER B 154 " --> pdb=" O THR B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 179 Processing helix chain 'B' and resid 183 through 195 Processing helix chain 'B' and resid 201 through 207 Processing helix chain 'B' and resid 227 through 244 Processing helix chain 'B' and resid 272 through 286 Processing helix chain 'B' and resid 307 through 313 Processing helix chain 'B' and resid 320 through 324 Processing helix chain 'B' and resid 335 through 344 removed outlier: 3.965A pdb=" N MET B 339 " --> pdb=" O PRO B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 377 Processing helix chain 'B' and resid 386 through 400 Processing helix chain 'B' and resid 408 through 414 Processing helix chain 'B' and resid 463 through 482 removed outlier: 3.516A pdb=" N ALA B 467 " --> pdb=" O PHE B 463 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU B 468 " --> pdb=" O LYS B 464 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASP B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 498 removed outlier: 4.237A pdb=" N CYS B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU B 493 " --> pdb=" O PRO B 489 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER B 494 " --> pdb=" O GLU B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 515 removed outlier: 3.776A pdb=" N ALA B 511 " --> pdb=" O GLY B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 551 removed outlier: 3.972A pdb=" N GLN B 525 " --> pdb=" O SER B 521 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS B 529 " --> pdb=" O GLN B 525 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU B 549 " --> pdb=" O ASP B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 571 removed outlier: 3.668A pdb=" N MET B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 592 removed outlier: 4.080A pdb=" N LEU B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 612 removed outlier: 3.556A pdb=" N ALA B 608 " --> pdb=" O THR B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 649 removed outlier: 3.674A pdb=" N GLU B 647 " --> pdb=" O LYS B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 661 removed outlier: 4.060A pdb=" N ALA B 661 " --> pdb=" O ASN B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 669 removed outlier: 3.846A pdb=" N SER B 668 " --> pdb=" O SER B 665 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 669 " --> pdb=" O ILE B 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 665 through 669' Processing helix chain 'B' and resid 675 through 680 Processing helix chain 'B' and resid 682 through 686 Processing helix chain 'B' and resid 687 through 701 removed outlier: 3.939A pdb=" N VAL B 691 " --> pdb=" O SER B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 731 Processing helix chain 'C' and resid 15 through 23 removed outlier: 3.883A pdb=" N THR C 19 " --> pdb=" O PHE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 27 removed outlier: 4.272A pdb=" N TYR C 27 " --> pdb=" O LYS C 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 24 through 27' Processing helix chain 'C' and resid 35 through 47 removed outlier: 4.017A pdb=" N ILE C 39 " --> pdb=" O ASP C 35 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY C 46 " --> pdb=" O LYS C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 68 removed outlier: 3.750A pdb=" N LEU C 56 " --> pdb=" O THR C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 71 No H-bonds generated for 'chain 'C' and resid 69 through 71' Processing helix chain 'C' and resid 72 through 90 removed outlier: 4.266A pdb=" N ILE C 76 " --> pdb=" O PRO C 72 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU C 89 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 103 removed outlier: 3.613A pdb=" N VAL C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 127 Processing helix chain 'C' and resid 127 through 135 removed outlier: 3.603A pdb=" N SER C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C 135 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 143 removed outlier: 3.731A pdb=" N ARG C 139 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP C 140 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE C 141 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR C 143 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 155 removed outlier: 3.940A pdb=" N SER C 154 " --> pdb=" O THR C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 179 Processing helix chain 'C' and resid 183 through 195 Processing helix chain 'C' and resid 201 through 207 Processing helix chain 'C' and resid 227 through 244 Processing helix chain 'C' and resid 272 through 286 Processing helix chain 'C' and resid 307 through 313 Processing helix chain 'C' and resid 320 through 324 Processing helix chain 'C' and resid 335 through 344 removed outlier: 3.964A pdb=" N MET C 339 " --> pdb=" O PRO C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 377 Processing helix chain 'C' and resid 386 through 400 Processing helix chain 'C' and resid 408 through 414 Processing helix chain 'C' and resid 463 through 482 removed outlier: 3.517A pdb=" N ALA C 467 " --> pdb=" O PHE C 463 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU C 468 " --> pdb=" O LYS C 464 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASP C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 498 removed outlier: 4.238A pdb=" N CYS C 492 " --> pdb=" O VAL C 488 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU C 493 " --> pdb=" O PRO C 489 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER C 494 " --> pdb=" O GLU C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 515 removed outlier: 3.776A pdb=" N ALA C 511 " --> pdb=" O GLY C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 551 removed outlier: 3.971A pdb=" N GLN C 525 " --> pdb=" O SER C 521 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS C 529 " --> pdb=" O GLN C 525 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU C 549 " --> pdb=" O ASP C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 571 removed outlier: 3.668A pdb=" N MET C 570 " --> pdb=" O LEU C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 592 removed outlier: 4.079A pdb=" N LEU C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 612 removed outlier: 3.556A pdb=" N ALA C 608 " --> pdb=" O THR C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 649 removed outlier: 3.674A pdb=" N GLU C 647 " --> pdb=" O LYS C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 661 removed outlier: 4.060A pdb=" N ALA C 661 " --> pdb=" O ASN C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 669 removed outlier: 3.845A pdb=" N SER C 668 " --> pdb=" O SER C 665 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 669 " --> pdb=" O ILE C 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 665 through 669' Processing helix chain 'C' and resid 675 through 680 Processing helix chain 'C' and resid 682 through 686 Processing helix chain 'C' and resid 687 through 701 removed outlier: 3.939A pdb=" N VAL C 691 " --> pdb=" O SER C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 731 Processing helix chain 'D' and resid 15 through 23 removed outlier: 3.882A pdb=" N THR D 19 " --> pdb=" O PHE D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 27 removed outlier: 4.272A pdb=" N TYR D 27 " --> pdb=" O LYS D 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 24 through 27' Processing helix chain 'D' and resid 35 through 47 removed outlier: 4.018A pdb=" N ILE D 39 " --> pdb=" O ASP D 35 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY D 46 " --> pdb=" O LYS D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 68 removed outlier: 3.751A pdb=" N LEU D 56 " --> pdb=" O THR D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 71 No H-bonds generated for 'chain 'D' and resid 69 through 71' Processing helix chain 'D' and resid 72 through 90 removed outlier: 4.266A pdb=" N ILE D 76 " --> pdb=" O PRO D 72 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU D 89 " --> pdb=" O ASN D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 103 removed outlier: 3.615A pdb=" N VAL D 97 " --> pdb=" O VAL D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 127 Processing helix chain 'D' and resid 127 through 135 removed outlier: 3.603A pdb=" N SER D 133 " --> pdb=" O ASP D 129 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE D 135 " --> pdb=" O LEU D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 143 removed outlier: 3.731A pdb=" N ARG D 139 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP D 140 " --> pdb=" O TYR D 137 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE D 141 " --> pdb=" O ASP D 138 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR D 143 " --> pdb=" O ASP D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 155 removed outlier: 3.940A pdb=" N SER D 154 " --> pdb=" O THR D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 179 Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 201 through 207 Processing helix chain 'D' and resid 227 through 244 Processing helix chain 'D' and resid 272 through 286 Processing helix chain 'D' and resid 307 through 313 Processing helix chain 'D' and resid 320 through 324 Processing helix chain 'D' and resid 335 through 344 removed outlier: 3.965A pdb=" N MET D 339 " --> pdb=" O PRO D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 377 Processing helix chain 'D' and resid 386 through 400 Processing helix chain 'D' and resid 408 through 414 Processing helix chain 'D' and resid 463 through 482 removed outlier: 3.516A pdb=" N ALA D 467 " --> pdb=" O PHE D 463 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU D 468 " --> pdb=" O LYS D 464 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASP D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 498 removed outlier: 4.238A pdb=" N CYS D 492 " --> pdb=" O VAL D 488 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU D 493 " --> pdb=" O PRO D 489 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER D 494 " --> pdb=" O GLU D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 515 removed outlier: 3.776A pdb=" N ALA D 511 " --> pdb=" O GLY D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 551 removed outlier: 3.971A pdb=" N GLN D 525 " --> pdb=" O SER D 521 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS D 529 " --> pdb=" O GLN D 525 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU D 549 " --> pdb=" O ASP D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 571 removed outlier: 3.668A pdb=" N MET D 570 " --> pdb=" O LEU D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 592 removed outlier: 4.081A pdb=" N LEU D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 612 removed outlier: 3.557A pdb=" N ALA D 608 " --> pdb=" O THR D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 649 removed outlier: 3.674A pdb=" N GLU D 647 " --> pdb=" O LYS D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 661 removed outlier: 4.060A pdb=" N ALA D 661 " --> pdb=" O ASN D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 669 removed outlier: 3.846A pdb=" N SER D 668 " --> pdb=" O SER D 665 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 669 " --> pdb=" O ILE D 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 665 through 669' Processing helix chain 'D' and resid 675 through 680 Processing helix chain 'D' and resid 682 through 686 Processing helix chain 'D' and resid 687 through 701 removed outlier: 3.938A pdb=" N VAL D 691 " --> pdb=" O SER D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 731 Processing helix chain 'E' and resid 15 through 23 removed outlier: 3.883A pdb=" N THR E 19 " --> pdb=" O PHE E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 27 removed outlier: 4.271A pdb=" N TYR E 27 " --> pdb=" O LYS E 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 24 through 27' Processing helix chain 'E' and resid 35 through 47 removed outlier: 4.017A pdb=" N ILE E 39 " --> pdb=" O ASP E 35 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY E 46 " --> pdb=" O LYS E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 68 removed outlier: 3.751A pdb=" N LEU E 56 " --> pdb=" O THR E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 71 No H-bonds generated for 'chain 'E' and resid 69 through 71' Processing helix chain 'E' and resid 72 through 90 removed outlier: 4.266A pdb=" N ILE E 76 " --> pdb=" O PRO E 72 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU E 89 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 103 removed outlier: 3.614A pdb=" N VAL E 97 " --> pdb=" O VAL E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 127 Processing helix chain 'E' and resid 127 through 135 removed outlier: 3.604A pdb=" N SER E 133 " --> pdb=" O ASP E 129 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE E 135 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 143 removed outlier: 3.732A pdb=" N ARG E 139 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP E 140 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE E 141 " --> pdb=" O ASP E 138 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR E 143 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 155 removed outlier: 3.941A pdb=" N SER E 154 " --> pdb=" O THR E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 179 Processing helix chain 'E' and resid 183 through 195 Processing helix chain 'E' and resid 201 through 207 Processing helix chain 'E' and resid 227 through 244 Processing helix chain 'E' and resid 272 through 286 Processing helix chain 'E' and resid 307 through 313 Processing helix chain 'E' and resid 320 through 324 Processing helix chain 'E' and resid 335 through 344 removed outlier: 3.965A pdb=" N MET E 339 " --> pdb=" O PRO E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 377 Processing helix chain 'E' and resid 386 through 400 Processing helix chain 'E' and resid 408 through 414 Processing helix chain 'E' and resid 463 through 482 removed outlier: 3.517A pdb=" N ALA E 467 " --> pdb=" O PHE E 463 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU E 468 " --> pdb=" O LYS E 464 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASP E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 498 removed outlier: 4.238A pdb=" N CYS E 492 " --> pdb=" O VAL E 488 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU E 493 " --> pdb=" O PRO E 489 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER E 494 " --> pdb=" O GLU E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 515 removed outlier: 3.776A pdb=" N ALA E 511 " --> pdb=" O GLY E 507 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 551 removed outlier: 3.972A pdb=" N GLN E 525 " --> pdb=" O SER E 521 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS E 529 " --> pdb=" O GLN E 525 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU E 549 " --> pdb=" O ASP E 545 " (cutoff:3.500A) Processing helix chain 'E' and resid 566 through 571 removed outlier: 3.669A pdb=" N MET E 570 " --> pdb=" O LEU E 566 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 592 removed outlier: 4.080A pdb=" N LEU E 584 " --> pdb=" O ASP E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 604 through 612 removed outlier: 3.556A pdb=" N ALA E 608 " --> pdb=" O THR E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 649 removed outlier: 3.673A pdb=" N GLU E 647 " --> pdb=" O LYS E 643 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 661 removed outlier: 4.060A pdb=" N ALA E 661 " --> pdb=" O ASN E 657 " (cutoff:3.500A) Processing helix chain 'E' and resid 665 through 669 removed outlier: 3.846A pdb=" N SER E 668 " --> pdb=" O SER E 665 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE E 669 " --> pdb=" O ILE E 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 665 through 669' Processing helix chain 'E' and resid 675 through 680 Processing helix chain 'E' and resid 682 through 686 Processing helix chain 'E' and resid 687 through 701 removed outlier: 3.939A pdb=" N VAL E 691 " --> pdb=" O SER E 687 " (cutoff:3.500A) Processing helix chain 'E' and resid 716 through 731 Processing helix chain 'F' and resid 15 through 23 removed outlier: 3.883A pdb=" N THR F 19 " --> pdb=" O PHE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 27 removed outlier: 4.272A pdb=" N TYR F 27 " --> pdb=" O LYS F 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 24 through 27' Processing helix chain 'F' and resid 35 through 47 removed outlier: 4.017A pdb=" N ILE F 39 " --> pdb=" O ASP F 35 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY F 46 " --> pdb=" O LYS F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 68 removed outlier: 3.751A pdb=" N LEU F 56 " --> pdb=" O THR F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 71 No H-bonds generated for 'chain 'F' and resid 69 through 71' Processing helix chain 'F' and resid 72 through 90 removed outlier: 4.266A pdb=" N ILE F 76 " --> pdb=" O PRO F 72 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU F 89 " --> pdb=" O ASN F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 103 removed outlier: 3.614A pdb=" N VAL F 97 " --> pdb=" O VAL F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 127 Processing helix chain 'F' and resid 127 through 135 removed outlier: 3.603A pdb=" N SER F 133 " --> pdb=" O ASP F 129 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE F 135 " --> pdb=" O LEU F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 143 removed outlier: 3.732A pdb=" N ARG F 139 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP F 140 " --> pdb=" O TYR F 137 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE F 141 " --> pdb=" O ASP F 138 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR F 143 " --> pdb=" O ASP F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 155 removed outlier: 3.940A pdb=" N SER F 154 " --> pdb=" O THR F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 179 Processing helix chain 'F' and resid 183 through 195 Processing helix chain 'F' and resid 201 through 207 Processing helix chain 'F' and resid 227 through 244 Processing helix chain 'F' and resid 272 through 286 Processing helix chain 'F' and resid 307 through 313 Processing helix chain 'F' and resid 320 through 324 Processing helix chain 'F' and resid 335 through 344 removed outlier: 3.964A pdb=" N MET F 339 " --> pdb=" O PRO F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 377 Processing helix chain 'F' and resid 386 through 400 Processing helix chain 'F' and resid 408 through 414 Processing helix chain 'F' and resid 463 through 482 removed outlier: 3.518A pdb=" N ALA F 467 " --> pdb=" O PHE F 463 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU F 468 " --> pdb=" O LYS F 464 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASP F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 498 removed outlier: 4.238A pdb=" N CYS F 492 " --> pdb=" O VAL F 488 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU F 493 " --> pdb=" O PRO F 489 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER F 494 " --> pdb=" O GLU F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 507 through 515 removed outlier: 3.776A pdb=" N ALA F 511 " --> pdb=" O GLY F 507 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 551 removed outlier: 3.972A pdb=" N GLN F 525 " --> pdb=" O SER F 521 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS F 529 " --> pdb=" O GLN F 525 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU F 549 " --> pdb=" O ASP F 545 " (cutoff:3.500A) Processing helix chain 'F' and resid 566 through 571 removed outlier: 3.668A pdb=" N MET F 570 " --> pdb=" O LEU F 566 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 592 removed outlier: 4.079A pdb=" N LEU F 584 " --> pdb=" O ASP F 580 " (cutoff:3.500A) Processing helix chain 'F' and resid 604 through 612 removed outlier: 3.556A pdb=" N ALA F 608 " --> pdb=" O THR F 604 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 649 removed outlier: 3.674A pdb=" N GLU F 647 " --> pdb=" O LYS F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 654 through 661 removed outlier: 4.060A pdb=" N ALA F 661 " --> pdb=" O ASN F 657 " (cutoff:3.500A) Processing helix chain 'F' and resid 665 through 669 removed outlier: 3.846A pdb=" N SER F 668 " --> pdb=" O SER F 665 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE F 669 " --> pdb=" O ILE F 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 665 through 669' Processing helix chain 'F' and resid 675 through 680 Processing helix chain 'F' and resid 682 through 686 Processing helix chain 'F' and resid 687 through 701 removed outlier: 3.939A pdb=" N VAL F 691 " --> pdb=" O SER F 687 " (cutoff:3.500A) Processing helix chain 'F' and resid 716 through 731 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 158 through 159 Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 200 removed outlier: 5.871A pdb=" N ALA A 447 " --> pdb=" O GLY A 504 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N GLN A 506 " --> pdb=" O ALA A 447 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU A 449 " --> pdb=" O GLN A 506 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 442 through 444 removed outlier: 6.924A pdb=" N ILE A 248 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N TYR A 300 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 250 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N MET A 405 " --> pdb=" O GLY A 735 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 287 through 288 removed outlier: 3.841A pdb=" N ARG A 293 " --> pdb=" O GLN A 288 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA7, first strand: chain 'A' and resid 624 through 629 Processing sheet with id=AA8, first strand: chain 'A' and resid 709 through 711 removed outlier: 6.749A pdb=" N ILE A 710 " --> pdb=" O ARG A 740 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 2 through 5 Processing sheet with id=AB1, first strand: chain 'B' and resid 158 through 159 Processing sheet with id=AB2, first strand: chain 'B' and resid 198 through 200 removed outlier: 5.872A pdb=" N ALA B 447 " --> pdb=" O GLY B 504 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLN B 506 " --> pdb=" O ALA B 447 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU B 449 " --> pdb=" O GLN B 506 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 442 through 444 removed outlier: 6.923A pdb=" N ILE B 248 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N TYR B 300 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B 250 " --> pdb=" O TYR B 300 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N MET B 405 " --> pdb=" O GLY B 735 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 287 through 288 removed outlier: 3.841A pdb=" N ARG B 293 " --> pdb=" O GLN B 288 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 347 through 350 Processing sheet with id=AB6, first strand: chain 'B' and resid 624 through 629 Processing sheet with id=AB7, first strand: chain 'B' and resid 709 through 711 removed outlier: 6.749A pdb=" N ILE B 710 " --> pdb=" O ARG B 740 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 2 through 5 Processing sheet with id=AB9, first strand: chain 'C' and resid 158 through 159 Processing sheet with id=AC1, first strand: chain 'C' and resid 198 through 200 removed outlier: 5.872A pdb=" N ALA C 447 " --> pdb=" O GLY C 504 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLN C 506 " --> pdb=" O ALA C 447 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU C 449 " --> pdb=" O GLN C 506 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 442 through 444 removed outlier: 6.924A pdb=" N ILE C 248 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N TYR C 300 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL C 250 " --> pdb=" O TYR C 300 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N MET C 405 " --> pdb=" O GLY C 735 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 287 through 288 removed outlier: 3.840A pdb=" N ARG C 293 " --> pdb=" O GLN C 288 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 347 through 350 Processing sheet with id=AC5, first strand: chain 'C' and resid 624 through 629 Processing sheet with id=AC6, first strand: chain 'C' and resid 709 through 711 removed outlier: 6.749A pdb=" N ILE C 710 " --> pdb=" O ARG C 740 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 2 through 5 Processing sheet with id=AC8, first strand: chain 'D' and resid 158 through 159 Processing sheet with id=AC9, first strand: chain 'D' and resid 198 through 200 removed outlier: 5.871A pdb=" N ALA D 447 " --> pdb=" O GLY D 504 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLN D 506 " --> pdb=" O ALA D 447 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU D 449 " --> pdb=" O GLN D 506 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 442 through 444 removed outlier: 6.923A pdb=" N ILE D 248 " --> pdb=" O ALA D 298 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N TYR D 300 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL D 250 " --> pdb=" O TYR D 300 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N MET D 405 " --> pdb=" O GLY D 735 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 287 through 288 removed outlier: 3.840A pdb=" N ARG D 293 " --> pdb=" O GLN D 288 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AD4, first strand: chain 'D' and resid 624 through 629 Processing sheet with id=AD5, first strand: chain 'D' and resid 709 through 711 removed outlier: 6.749A pdb=" N ILE D 710 " --> pdb=" O ARG D 740 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'E' and resid 2 through 5 Processing sheet with id=AD7, first strand: chain 'E' and resid 158 through 159 Processing sheet with id=AD8, first strand: chain 'E' and resid 198 through 200 removed outlier: 5.871A pdb=" N ALA E 447 " --> pdb=" O GLY E 504 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N GLN E 506 " --> pdb=" O ALA E 447 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU E 449 " --> pdb=" O GLN E 506 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 442 through 444 removed outlier: 6.924A pdb=" N ILE E 248 " --> pdb=" O ALA E 298 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N TYR E 300 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL E 250 " --> pdb=" O TYR E 300 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N MET E 405 " --> pdb=" O GLY E 735 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 287 through 288 removed outlier: 3.840A pdb=" N ARG E 293 " --> pdb=" O GLN E 288 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 347 through 350 Processing sheet with id=AE3, first strand: chain 'E' and resid 624 through 629 Processing sheet with id=AE4, first strand: chain 'E' and resid 709 through 711 removed outlier: 6.749A pdb=" N ILE E 710 " --> pdb=" O ARG E 740 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'F' and resid 2 through 5 Processing sheet with id=AE6, first strand: chain 'F' and resid 158 through 159 Processing sheet with id=AE7, first strand: chain 'F' and resid 198 through 200 removed outlier: 5.870A pdb=" N ALA F 447 " --> pdb=" O GLY F 504 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLN F 506 " --> pdb=" O ALA F 447 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU F 449 " --> pdb=" O GLN F 506 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 442 through 444 removed outlier: 6.924A pdb=" N ILE F 248 " --> pdb=" O ALA F 298 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N TYR F 300 " --> pdb=" O ILE F 248 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL F 250 " --> pdb=" O TYR F 300 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N MET F 405 " --> pdb=" O GLY F 735 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 287 through 288 removed outlier: 3.840A pdb=" N ARG F 293 " --> pdb=" O GLN F 288 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 347 through 350 Processing sheet with id=AF2, first strand: chain 'F' and resid 624 through 629 Processing sheet with id=AF3, first strand: chain 'F' and resid 709 through 711 removed outlier: 6.749A pdb=" N ILE F 710 " --> pdb=" O ARG F 740 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 1626 hydrogen bonds defined for protein. 4644 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: 7.73 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7868 1.33 - 1.45: 8201 1.45 - 1.57: 20591 1.57 - 1.69: 78 1.69 - 1.81: 330 Bond restraints: 37068 Sorted by residual: bond pdb=" O3A CDP E 805 " pdb=" PB CDP E 805 " ideal model delta sigma weight residual 1.748 1.594 0.154 2.00e-02 2.50e+03 5.95e+01 bond pdb=" O3A CDP C 805 " pdb=" PB CDP C 805 " ideal model delta sigma weight residual 1.748 1.595 0.153 2.00e-02 2.50e+03 5.88e+01 bond pdb=" O3A CDP F 805 " pdb=" PB CDP F 805 " ideal model delta sigma weight residual 1.748 1.595 0.153 2.00e-02 2.50e+03 5.86e+01 bond pdb=" O3A CDP D 805 " pdb=" PB CDP D 805 " ideal model delta sigma weight residual 1.748 1.595 0.153 2.00e-02 2.50e+03 5.85e+01 bond pdb=" O3A CDP B 805 " pdb=" PB CDP B 805 " ideal model delta sigma weight residual 1.748 1.595 0.153 2.00e-02 2.50e+03 5.82e+01 ... (remaining 37063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.73: 50029 4.73 - 9.46: 243 9.46 - 14.19: 14 14.19 - 18.92: 6 18.92 - 23.65: 18 Bond angle restraints: 50310 Sorted by residual: angle pdb=" PA DTP F 801 " pdb=" O3A DTP F 801 " pdb=" PB DTP F 801 " ideal model delta sigma weight residual 136.83 113.18 23.65 1.00e+00 1.00e+00 5.59e+02 angle pdb=" PA DTP D 801 " pdb=" O3A DTP D 801 " pdb=" PB DTP D 801 " ideal model delta sigma weight residual 136.83 113.39 23.44 1.00e+00 1.00e+00 5.49e+02 angle pdb=" PB DTP B 803 " pdb=" O3B DTP B 803 " pdb=" PG DTP B 803 " ideal model delta sigma weight residual 139.87 116.90 22.97 1.00e+00 1.00e+00 5.28e+02 angle pdb=" PA DTP B 801 " pdb=" O3A DTP B 801 " pdb=" PB DTP B 801 " ideal model delta sigma weight residual 136.83 114.09 22.74 1.00e+00 1.00e+00 5.17e+02 angle pdb=" PB DTP E 803 " pdb=" O3B DTP E 803 " pdb=" PG DTP E 803 " ideal model delta sigma weight residual 139.87 117.14 22.73 1.00e+00 1.00e+00 5.17e+02 ... (remaining 50305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.59: 22057 28.59 - 57.18: 185 57.18 - 85.78: 21 85.78 - 114.37: 3 114.37 - 142.96: 6 Dihedral angle restraints: 22272 sinusoidal: 9150 harmonic: 13122 Sorted by residual: dihedral pdb=" CA GLU A 615 " pdb=" C GLU A 615 " pdb=" N SER A 616 " pdb=" CA SER A 616 " ideal model delta harmonic sigma weight residual -180.00 -142.28 -37.72 0 5.00e+00 4.00e-02 5.69e+01 dihedral pdb=" CA GLU D 615 " pdb=" C GLU D 615 " pdb=" N SER D 616 " pdb=" CA SER D 616 " ideal model delta harmonic sigma weight residual -180.00 -142.29 -37.71 0 5.00e+00 4.00e-02 5.69e+01 dihedral pdb=" CA GLU E 615 " pdb=" C GLU E 615 " pdb=" N SER E 616 " pdb=" CA SER E 616 " ideal model delta harmonic sigma weight residual -180.00 -142.29 -37.71 0 5.00e+00 4.00e-02 5.69e+01 ... (remaining 22269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3583 0.049 - 0.097: 1470 0.097 - 0.146: 414 0.146 - 0.194: 41 0.194 - 0.243: 18 Chirality restraints: 5526 Sorted by residual: chirality pdb=" CB ILE D 659 " pdb=" CA ILE D 659 " pdb=" CG1 ILE D 659 " pdb=" CG2 ILE D 659 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE A 659 " pdb=" CA ILE A 659 " pdb=" CG1 ILE A 659 " pdb=" CG2 ILE A 659 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB ILE C 659 " pdb=" CA ILE C 659 " pdb=" CG1 ILE C 659 " pdb=" CG2 ILE C 659 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 5523 not shown) Planarity restraints: 6336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 669 " 0.054 5.00e-02 4.00e+02 8.16e-02 1.06e+01 pdb=" N PRO B 670 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO B 670 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 670 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 669 " -0.053 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO F 670 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO F 670 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO F 670 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 669 " -0.053 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO A 670 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 670 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 670 " -0.045 5.00e-02 4.00e+02 ... (remaining 6333 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 460 2.60 - 3.17: 30363 3.17 - 3.75: 54935 3.75 - 4.32: 80308 4.32 - 4.90: 129472 Nonbonded interactions: 295538 Sorted by model distance: nonbonded pdb=" O2B DTP F 803 " pdb="MG MG F 804 " model vdw 2.024 2.170 nonbonded pdb=" O2B DTP D 803 " pdb="MG MG D 804 " model vdw 2.025 2.170 nonbonded pdb=" O1B DTP A 803 " pdb="MG MG A 804 " model vdw 2.028 2.170 nonbonded pdb=" O1B DTP E 803 " pdb="MG MG E 804 " model vdw 2.029 2.170 nonbonded pdb=" O1B DTP C 803 " pdb="MG MG C 804 " model vdw 2.034 2.170 ... (remaining 295533 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 0.480 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 31.670 Find NCS groups from input model: 0.290 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 : 0.008 0.154 37068 Z= 0.373 Angle : 1.089 23.651 50310 Z= 0.735 Chirality : 0.055 0.243 5526 Planarity : 0.007 0.082 6336 Dihedral : 10.026 142.960 13848 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.97 (0.10), residues: 4458 helix: -3.11 (0.07), residues: 2160 sheet: -1.70 (0.26), residues: 336 loop : -2.04 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 196 TYR 0.041 0.003 TYR F 300 PHE 0.021 0.003 PHE D 198 TRP 0.020 0.003 TRP E 390 HIS 0.008 0.002 HIS B 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00765 / 0.37 (37068) covalent geometry : angle 1.08886 / 0.74 (50310) hydrogen bonds : bond 0.13252 / 8.59 ( 1626) hydrogen bonds : angle 9.53605 / 6.63 ( 4644) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1097 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1097 time to evaluate : 1.425 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7415 (mtt) cc_final: 0.6769 (mtt) REVERT: A 26 CYS cc_start: 0.6897 (m) cc_final: 0.6642 (m) REVERT: A 62 GLU cc_start: 0.8220 (tt0) cc_final: 0.7913 (tm-30) REVERT: A 149 LYS cc_start: 0.8057 (tttt) cc_final: 0.7775 (tppt) REVERT: A 151 LEU cc_start: 0.8821 (tp) cc_final: 0.8548 (tt) REVERT: A 170 MET cc_start: 0.8071 (ttp) cc_final: 0.7818 (ttm) REVERT: A 175 SER cc_start: 0.8797 (m) cc_final: 0.8531 (t) REVERT: A 233 ASP cc_start: 0.7894 (m-30) cc_final: 0.7214 (m-30) REVERT: A 286 VAL cc_start: 0.8891 (t) cc_final: 0.8667 (m) REVERT: A 423 ILE cc_start: 0.9574 (mt) cc_final: 0.9311 (mm) REVERT: A 425 CYS cc_start: 0.8749 (p) cc_final: 0.8497 (p) REVERT: A 429 CYS cc_start: 0.7767 (m) cc_final: 0.7482 (m) REVERT: A 432 ILE cc_start: 0.8370 (mm) cc_final: 0.7872 (tp) REVERT: A 443 VAL cc_start: 0.9094 (t) cc_final: 0.8816 (t) REVERT: A 625 TYR cc_start: 0.7436 (p90) cc_final: 0.7209 (p90) REVERT: A 655 MET cc_start: 0.8206 (tpt) cc_final: 0.7722 (tpp) REVERT: A 677 LYS cc_start: 0.7748 (mttt) cc_final: 0.6948 (tptt) REVERT: A 708 LEU cc_start: 0.7971 (tp) cc_final: 0.7719 (mp) REVERT: A 739 LEU cc_start: 0.8703 (tp) cc_final: 0.8361 (tp) REVERT: B 149 LYS cc_start: 0.8185 (tttt) cc_final: 0.7686 (tppt) REVERT: B 172 MET cc_start: 0.7869 (tpp) cc_final: 0.7653 (tpp) REVERT: B 175 SER cc_start: 0.8865 (m) cc_final: 0.8579 (t) REVERT: B 189 THR cc_start: 0.7987 (m) cc_final: 0.7508 (m) REVERT: B 253 SER cc_start: 0.9027 (m) cc_final: 0.8826 (t) REVERT: B 433 VAL cc_start: 0.8845 (t) cc_final: 0.8585 (m) REVERT: B 643 LYS cc_start: 0.9113 (tttt) cc_final: 0.8911 (ttmm) REVERT: B 694 MET cc_start: 0.8004 (mtp) cc_final: 0.7748 (mtt) REVERT: B 708 LEU cc_start: 0.8228 (tp) cc_final: 0.7977 (mp) REVERT: C 16 ASP cc_start: 0.7069 (m-30) cc_final: 0.6605 (t0) REVERT: C 26 CYS cc_start: 0.7413 (m) cc_final: 0.7152 (m) REVERT: C 38 GLN cc_start: 0.8896 (mt0) cc_final: 0.8507 (mt0) REVERT: C 52 THR cc_start: 0.8699 (m) cc_final: 0.8339 (p) REVERT: C 223 MET cc_start: 0.8531 (mmt) cc_final: 0.8327 (mmm) REVERT: C 328 LEU cc_start: 0.8796 (mt) cc_final: 0.8523 (tp) REVERT: C 361 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7763 (tm-30) REVERT: C 432 ILE cc_start: 0.8527 (mm) cc_final: 0.7695 (tp) REVERT: C 433 VAL cc_start: 0.8855 (t) cc_final: 0.8644 (m) REVERT: C 438 LYS cc_start: 0.8886 (mttt) cc_final: 0.8297 (mptt) REVERT: C 443 VAL cc_start: 0.9114 (t) cc_final: 0.8838 (t) REVERT: C 444 CYS cc_start: 0.7424 (t) cc_final: 0.7134 (t) REVERT: C 493 LEU cc_start: 0.7553 (tp) cc_final: 0.7351 (mt) REVERT: C 497 ARG cc_start: 0.7958 (mtp180) cc_final: 0.7700 (mtp85) REVERT: C 515 MET cc_start: 0.7855 (mmm) cc_final: 0.7569 (tpp) REVERT: C 655 MET cc_start: 0.8485 (tpt) cc_final: 0.7920 (tpp) REVERT: C 677 LYS cc_start: 0.7263 (mttt) cc_final: 0.6630 (tptt) REVERT: C 694 MET cc_start: 0.7993 (mtp) cc_final: 0.7755 (mtt) REVERT: C 708 LEU cc_start: 0.7980 (tp) cc_final: 0.7495 (mt) REVERT: C 726 TYR cc_start: 0.8771 (t80) cc_final: 0.7687 (t80) REVERT: C 739 LEU cc_start: 0.8657 (tp) cc_final: 0.8369 (tp) REVERT: D 38 GLN cc_start: 0.8774 (mt0) cc_final: 0.8492 (mt0) REVERT: D 149 LYS cc_start: 0.8251 (tttt) cc_final: 0.7996 (tppt) REVERT: D 157 LEU cc_start: 0.9067 (mt) cc_final: 0.8797 (mp) REVERT: D 165 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7443 (mt-10) REVERT: D 175 SER cc_start: 0.8426 (m) cc_final: 0.8181 (t) REVERT: D 223 MET cc_start: 0.8397 (mmt) cc_final: 0.8128 (mmt) REVERT: D 429 CYS cc_start: 0.8098 (m) cc_final: 0.7834 (m) REVERT: D 432 ILE cc_start: 0.8563 (mm) cc_final: 0.7799 (tp) REVERT: D 433 VAL cc_start: 0.8880 (t) cc_final: 0.8623 (m) REVERT: D 438 LYS cc_start: 0.8922 (mttt) cc_final: 0.8365 (mptt) REVERT: D 443 VAL cc_start: 0.9139 (t) cc_final: 0.8735 (t) REVERT: D 444 CYS cc_start: 0.7475 (t) cc_final: 0.7171 (t) REVERT: D 497 ARG cc_start: 0.8112 (mtp180) cc_final: 0.7732 (mtp85) REVERT: D 515 MET cc_start: 0.7907 (mmm) cc_final: 0.7473 (tpp) REVERT: D 655 MET cc_start: 0.8511 (tpt) cc_final: 0.7991 (tpp) REVERT: D 694 MET cc_start: 0.8152 (mtp) cc_final: 0.7888 (mtt) REVERT: D 708 LEU cc_start: 0.7991 (tp) cc_final: 0.7363 (mp) REVERT: D 739 LEU cc_start: 0.8685 (tp) cc_final: 0.8394 (tp) REVERT: E 149 LYS cc_start: 0.8198 (tttt) cc_final: 0.7920 (tppt) REVERT: E 175 SER cc_start: 0.8864 (m) cc_final: 0.8587 (t) REVERT: E 189 THR cc_start: 0.7873 (m) cc_final: 0.7401 (m) REVERT: E 433 VAL cc_start: 0.8944 (t) cc_final: 0.8647 (m) REVERT: E 677 LYS cc_start: 0.7409 (mttt) cc_final: 0.7130 (tptt) REVERT: E 694 MET cc_start: 0.7932 (mtp) cc_final: 0.7687 (mtt) REVERT: E 739 LEU cc_start: 0.8560 (tp) cc_final: 0.8329 (tp) REVERT: F 1 MET cc_start: 0.7338 (mtt) cc_final: 0.6670 (mtt) REVERT: F 26 CYS cc_start: 0.7101 (m) cc_final: 0.6766 (m) REVERT: F 39 ILE cc_start: 0.9217 (mt) cc_final: 0.8957 (pt) REVERT: F 411 CYS cc_start: 0.8321 (m) cc_final: 0.8091 (m) REVERT: F 423 ILE cc_start: 0.9584 (mt) cc_final: 0.9321 (mm) REVERT: F 432 ILE cc_start: 0.8429 (mm) cc_final: 0.8018 (tp) REVERT: F 534 THR cc_start: 0.8748 (m) cc_final: 0.8438 (p) REVERT: F 625 TYR cc_start: 0.7481 (p90) cc_final: 0.7280 (p90) REVERT: F 655 MET cc_start: 0.8253 (tpt) cc_final: 0.7757 (tpp) REVERT: F 694 MET cc_start: 0.7870 (mtp) cc_final: 0.7615 (mtt) REVERT: F 708 LEU cc_start: 0.8101 (tp) cc_final: 0.7793 (mp) REVERT: F 726 TYR cc_start: 0.8842 (t80) cc_final: 0.7787 (t80) REVERT: F 739 LEU cc_start: 0.8574 (tp) cc_final: 0.8294 (tp) outliers start: 0 outliers final: 0 residues processed: 1097 average time/residue: 0.2359 time to fit residues: 413.1487 Evaluate side-chains 637 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 637 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 0.0970 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.0980 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 ASN A 354 ASN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 ASN B 144 ASN B 354 ASN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN C 127 ASN C 354 ASN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 567 GLN C 657 ASN D 127 ASN D 354 ASN ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 567 GLN E 127 ASN E 354 ASN E 418 GLN ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 567 GLN E 706 GLN F 127 ASN F 345 ASN F 354 ASN ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 635 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.113062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.099989 restraints weight = 78612.835| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.98 r_work: 0.3406 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37068 Z= 0.120 Angle : 0.592 9.054 50310 Z= 0.311 Chirality : 0.044 0.163 5526 Planarity : 0.005 0.055 6336 Dihedral : 9.266 147.565 5124 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.31 % Allowed : 8.53 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.11), residues: 4458 helix: -0.90 (0.10), residues: 2226 sheet: -1.31 (0.25), residues: 306 loop : -1.45 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 9 TYR 0.026 0.002 TYR A 536 PHE 0.021 0.001 PHE C 519 TRP 0.013 0.001 TRP A 333 HIS 0.004 0.001 HIS B 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (37068) covalent geometry : angle 0.59250 / 0.31 (50310) hydrogen bonds : bond 0.04176 / 2.74 ( 1626) hydrogen bonds : angle 5.53730 / 3.88 ( 4644) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 736 time to evaluate : 1.298 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 21 ARG cc_start: 0.7200 (ttt180) cc_final: 0.6012 (mmt180) REVERT: A 23 GLN cc_start: 0.8446 (tt0) cc_final: 0.8018 (pt0) REVERT: A 149 LYS cc_start: 0.8134 (tttt) cc_final: 0.7921 (tppt) REVERT: A 225 ASP cc_start: 0.8498 (t70) cc_final: 0.8054 (t0) REVERT: A 361 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7873 (tm-30) REVERT: A 368 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7700 (tp30) REVERT: A 432 ILE cc_start: 0.8414 (mm) cc_final: 0.8111 (tp) REVERT: A 677 LYS cc_start: 0.7833 (mttt) cc_final: 0.7091 (tptt) REVERT: A 681 LYS cc_start: 0.8490 (mtpt) cc_final: 0.8161 (mtpp) REVERT: A 708 LEU cc_start: 0.8068 (tp) cc_final: 0.7856 (mp) REVERT: A 726 TYR cc_start: 0.8891 (t80) cc_final: 0.7940 (t80) REVERT: A 739 LEU cc_start: 0.8484 (tp) cc_final: 0.8270 (tp) REVERT: B 21 ARG cc_start: 0.6686 (ttt180) cc_final: 0.5756 (mmt-90) REVERT: B 23 GLN cc_start: 0.7407 (pt0) cc_final: 0.7176 (pt0) REVERT: B 57 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.7831 (m-30) REVERT: B 98 MET cc_start: 0.8779 (mmp) cc_final: 0.8429 (mmm) REVERT: B 165 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7634 (mt-10) REVERT: B 189 THR cc_start: 0.8712 (m) cc_final: 0.8451 (m) REVERT: B 253 SER cc_start: 0.9154 (m) cc_final: 0.8942 (t) REVERT: B 360 ASP cc_start: 0.8454 (p0) cc_final: 0.8063 (p0) REVERT: B 405 MET cc_start: 0.8802 (mtp) cc_final: 0.8428 (mtp) REVERT: B 433 VAL cc_start: 0.8992 (t) cc_final: 0.8784 (m) REVERT: B 453 MET cc_start: 0.6776 (mpp) cc_final: 0.6508 (mpp) REVERT: B 545 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8423 (m-30) REVERT: B 677 LYS cc_start: 0.7868 (mttt) cc_final: 0.7220 (tptt) REVERT: B 694 MET cc_start: 0.8270 (mtp) cc_final: 0.7999 (mtt) REVERT: B 708 LEU cc_start: 0.8337 (tp) cc_final: 0.8026 (mp) REVERT: B 726 TYR cc_start: 0.8812 (t80) cc_final: 0.7683 (t80) REVERT: C 14 MET cc_start: 0.8050 (mpp) cc_final: 0.7663 (mpp) REVERT: C 21 ARG cc_start: 0.7425 (ttt180) cc_final: 0.6398 (mmt180) REVERT: C 23 GLN cc_start: 0.8298 (tt0) cc_final: 0.7890 (pt0) REVERT: C 26 CYS cc_start: 0.8088 (m) cc_final: 0.7847 (p) REVERT: C 89 GLU cc_start: 0.8592 (tp30) cc_final: 0.8304 (tm-30) REVERT: C 152 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8195 (tm-30) REVERT: C 361 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8131 (tm-30) REVERT: C 368 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7923 (tp30) REVERT: C 432 ILE cc_start: 0.8734 (mm) cc_final: 0.7502 (tp) REVERT: C 438 LYS cc_start: 0.8872 (mttt) cc_final: 0.8664 (mptt) REVERT: C 453 MET cc_start: 0.7688 (tpt) cc_final: 0.7471 (tpp) REVERT: C 490 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8495 (mt-10) REVERT: C 493 LEU cc_start: 0.7683 (tp) cc_final: 0.7408 (mt) REVERT: C 515 MET cc_start: 0.7950 (mmm) cc_final: 0.7724 (mmt) REVERT: C 545 ASP cc_start: 0.8784 (OUTLIER) cc_final: 0.8179 (m-30) REVERT: C 634 PHE cc_start: 0.6781 (p90) cc_final: 0.6526 (p90) REVERT: C 655 MET cc_start: 0.8288 (tpt) cc_final: 0.7926 (tpp) REVERT: C 674 ASP cc_start: 0.7262 (m-30) cc_final: 0.6904 (t0) REVERT: C 677 LYS cc_start: 0.7299 (mttt) cc_final: 0.6671 (tptt) REVERT: C 681 LYS cc_start: 0.8339 (mtpt) cc_final: 0.8004 (mtpt) REVERT: C 692 LEU cc_start: 0.8589 (mt) cc_final: 0.8376 (mm) REVERT: C 694 MET cc_start: 0.8275 (mtp) cc_final: 0.7971 (mtt) REVERT: C 708 LEU cc_start: 0.8209 (tp) cc_final: 0.7869 (mp) REVERT: C 726 TYR cc_start: 0.8747 (t80) cc_final: 0.7533 (t80) REVERT: D 21 ARG cc_start: 0.6530 (ttt180) cc_final: 0.5735 (mmt180) REVERT: D 23 GLN cc_start: 0.8353 (tt0) cc_final: 0.7665 (pt0) REVERT: D 57 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.7817 (m-30) REVERT: D 165 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7741 (mt-10) REVERT: D 218 CYS cc_start: 0.7418 (m) cc_final: 0.6976 (m) REVERT: D 368 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7602 (tp30) REVERT: D 429 CYS cc_start: 0.8618 (m) cc_final: 0.8393 (m) REVERT: D 444 CYS cc_start: 0.7764 (t) cc_final: 0.6971 (t) REVERT: D 515 MET cc_start: 0.7850 (mmm) cc_final: 0.7521 (mmt) REVERT: D 655 MET cc_start: 0.8398 (tpt) cc_final: 0.7989 (tpp) REVERT: D 674 ASP cc_start: 0.7160 (m-30) cc_final: 0.6799 (t0) REVERT: D 677 LYS cc_start: 0.7378 (mttt) cc_final: 0.6766 (tptt) REVERT: D 681 LYS cc_start: 0.8360 (mtpt) cc_final: 0.7917 (mtpt) REVERT: D 694 MET cc_start: 0.8283 (mtp) cc_final: 0.7988 (mtt) REVERT: D 708 LEU cc_start: 0.8202 (tp) cc_final: 0.7835 (mp) REVERT: D 726 TYR cc_start: 0.8805 (t80) cc_final: 0.7691 (t80) REVERT: E 21 ARG cc_start: 0.6960 (ttt180) cc_final: 0.5911 (mmt-90) REVERT: E 23 GLN cc_start: 0.7459 (pt0) cc_final: 0.7191 (pt0) REVERT: E 98 MET cc_start: 0.8764 (mmp) cc_final: 0.8289 (mmm) REVERT: E 149 LYS cc_start: 0.8066 (tttt) cc_final: 0.7727 (tppt) REVERT: E 152 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8358 (tm-30) REVERT: E 189 THR cc_start: 0.8778 (m) cc_final: 0.8508 (m) REVERT: E 405 MET cc_start: 0.8812 (mtp) cc_final: 0.8439 (mtp) REVERT: E 423 ILE cc_start: 0.9436 (mt) cc_final: 0.9228 (mm) REVERT: E 433 VAL cc_start: 0.9048 (t) cc_final: 0.8811 (m) REVERT: E 434 GLU cc_start: 0.8046 (tt0) cc_final: 0.7803 (tm-30) REVERT: E 545 ASP cc_start: 0.8800 (OUTLIER) cc_final: 0.8543 (m-30) REVERT: E 634 PHE cc_start: 0.6927 (p90) cc_final: 0.6481 (p90) REVERT: E 677 LYS cc_start: 0.7712 (mttt) cc_final: 0.7209 (tptt) REVERT: E 693 LYS cc_start: 0.9029 (tptm) cc_final: 0.8804 (tptp) REVERT: E 694 MET cc_start: 0.8316 (mtp) cc_final: 0.8083 (mtt) REVERT: E 726 TYR cc_start: 0.8812 (t80) cc_final: 0.7629 (t80) REVERT: E 738 TYR cc_start: 0.8238 (m-80) cc_final: 0.7671 (m-80) REVERT: F 21 ARG cc_start: 0.7091 (ttt180) cc_final: 0.6177 (mmt180) REVERT: F 368 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7762 (tp30) REVERT: F 375 GLU cc_start: 0.7068 (tt0) cc_final: 0.6828 (mt-10) REVERT: F 432 ILE cc_start: 0.8500 (mm) cc_final: 0.8094 (tp) REVERT: F 625 TYR cc_start: 0.7584 (p90) cc_final: 0.7308 (p90) REVERT: F 655 MET cc_start: 0.8191 (tpt) cc_final: 0.7691 (tpp) REVERT: F 674 ASP cc_start: 0.7044 (m-30) cc_final: 0.6790 (t0) REVERT: F 677 LYS cc_start: 0.7944 (mttt) cc_final: 0.7215 (tptt) REVERT: F 681 LYS cc_start: 0.8269 (mtpt) cc_final: 0.7946 (mtpp) REVERT: F 694 MET cc_start: 0.8199 (mtp) cc_final: 0.7974 (mtt) REVERT: F 708 LEU cc_start: 0.8154 (tp) cc_final: 0.7871 (mp) REVERT: F 726 TYR cc_start: 0.8776 (t80) cc_final: 0.8501 (t80) outliers start: 51 outliers final: 18 residues processed: 769 average time/residue: 0.2155 time to fit residues: 271.4310 Evaluate side-chains 582 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 559 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 533 GLU Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 533 GLU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 418 GLN Chi-restraints excluded: chain E residue 545 ASP Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 627 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 96 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 283 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 358 optimal weight: 5.9990 chunk 257 optimal weight: 4.9990 chunk 370 optimal weight: 10.0000 chunk 289 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 ASN B 266 ASN B 418 GLN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 GLN C 38 GLN C 266 ASN C 567 GLN D 112 HIS D 266 ASN E 266 ASN E 418 GLN ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 266 ASN F 478 ASN ** F 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.103284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.090941 restraints weight = 79984.175| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.85 r_work: 0.3269 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.148 37068 Z= 0.308 Angle : 0.725 9.151 50310 Z= 0.379 Chirality : 0.050 0.176 5526 Planarity : 0.005 0.053 6336 Dihedral : 8.730 144.401 5124 Min Nonbonded Distance : 1.637 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.56 % Allowed : 11.06 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.12), residues: 4458 helix: -0.14 (0.11), residues: 2232 sheet: -1.03 (0.29), residues: 246 loop : -1.32 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 12 TYR 0.021 0.002 TYR E 190 PHE 0.021 0.003 PHE C 701 TRP 0.016 0.002 TRP E 333 HIS 0.008 0.001 HIS F 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00713 / 0.31 (37068) covalent geometry : angle 0.72494 / 0.38 (50310) hydrogen bonds : bond 0.05024 / 3.32 ( 1626) hydrogen bonds : angle 5.48804 / 3.85 ( 4644) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 560 time to evaluate : 1.432 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: symmetry clash REVERT: A 23 GLN cc_start: 0.8411 (tt0) cc_final: 0.7974 (pt0) REVERT: A 41 MET cc_start: 0.8703 (ttp) cc_final: 0.8492 (ttp) REVERT: A 89 GLU cc_start: 0.8679 (tp30) cc_final: 0.8335 (tm-30) REVERT: A 149 LYS cc_start: 0.8345 (tttt) cc_final: 0.8081 (tppt) REVERT: A 225 ASP cc_start: 0.8519 (t70) cc_final: 0.8010 (t0) REVERT: A 233 ASP cc_start: 0.8514 (m-30) cc_final: 0.7987 (m-30) REVERT: A 307 ASP cc_start: 0.8267 (t0) cc_final: 0.8058 (t0) REVERT: A 416 ASN cc_start: 0.8167 (t0) cc_final: 0.7732 (t0) REVERT: A 431 GLU cc_start: 0.7695 (pm20) cc_final: 0.7489 (pm20) REVERT: A 432 ILE cc_start: 0.8482 (mm) cc_final: 0.8197 (tp) REVERT: A 677 LYS cc_start: 0.7934 (mttt) cc_final: 0.7134 (tptt) REVERT: A 681 LYS cc_start: 0.8290 (mtpt) cc_final: 0.8033 (mtpp) REVERT: A 708 LEU cc_start: 0.8237 (tp) cc_final: 0.7940 (mt) REVERT: A 739 LEU cc_start: 0.8499 (tp) cc_final: 0.8230 (tp) REVERT: B 12 ARG cc_start: 0.6657 (mmt-90) cc_final: 0.6408 (mmp80) REVERT: B 21 ARG cc_start: 0.7281 (ttt180) cc_final: 0.6433 (mmt-90) REVERT: B 57 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.7919 (m-30) REVERT: B 172 MET cc_start: 0.8592 (tpt) cc_final: 0.8210 (mmm) REVERT: B 253 SER cc_start: 0.9253 (m) cc_final: 0.8974 (t) REVERT: B 388 GLN cc_start: 0.8319 (tp40) cc_final: 0.7924 (tp-100) REVERT: B 405 MET cc_start: 0.8936 (mtp) cc_final: 0.8560 (mtp) REVERT: B 431 GLU cc_start: 0.7507 (pm20) cc_final: 0.7256 (pm20) REVERT: B 433 VAL cc_start: 0.9224 (t) cc_final: 0.8948 (m) REVERT: B 545 ASP cc_start: 0.8860 (OUTLIER) cc_final: 0.8461 (m-30) REVERT: B 602 MET cc_start: 0.8962 (pmm) cc_final: 0.8636 (pmm) REVERT: B 610 ILE cc_start: 0.8899 (mt) cc_final: 0.8677 (tt) REVERT: B 634 PHE cc_start: 0.6925 (p90) cc_final: 0.6649 (p90) REVERT: B 677 LYS cc_start: 0.7477 (mttt) cc_final: 0.7165 (tptt) REVERT: B 694 MET cc_start: 0.8348 (mtp) cc_final: 0.8116 (mtt) REVERT: B 708 LEU cc_start: 0.8367 (tp) cc_final: 0.8056 (mt) REVERT: C 14 MET cc_start: 0.8348 (mpp) cc_final: 0.7484 (mpp) REVERT: C 23 GLN cc_start: 0.8372 (tt0) cc_final: 0.7810 (pt0) REVERT: C 57 ASP cc_start: 0.9059 (OUTLIER) cc_final: 0.8668 (m-30) REVERT: C 89 GLU cc_start: 0.8684 (tp30) cc_final: 0.8316 (tm-30) REVERT: C 149 LYS cc_start: 0.8197 (tttt) cc_final: 0.7884 (tppt) REVERT: C 152 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8221 (tm-30) REVERT: C 361 GLU cc_start: 0.8533 (mt-10) cc_final: 0.7996 (tm-30) REVERT: C 388 GLN cc_start: 0.8814 (tp-100) cc_final: 0.8422 (tp-100) REVERT: C 416 ASN cc_start: 0.7999 (t0) cc_final: 0.7686 (t0) REVERT: C 493 LEU cc_start: 0.7598 (tp) cc_final: 0.7343 (mt) REVERT: C 515 MET cc_start: 0.8097 (mmm) cc_final: 0.7843 (mmt) REVERT: C 655 MET cc_start: 0.8542 (tpt) cc_final: 0.8105 (tpp) REVERT: C 681 LYS cc_start: 0.8321 (mtpt) cc_final: 0.7902 (mtpt) REVERT: C 694 MET cc_start: 0.8372 (mtp) cc_final: 0.8117 (mtt) REVERT: C 708 LEU cc_start: 0.8423 (tp) cc_final: 0.7755 (mt) REVERT: C 726 TYR cc_start: 0.8811 (t80) cc_final: 0.8168 (t80) REVERT: D 23 GLN cc_start: 0.8445 (tt0) cc_final: 0.7815 (pt0) REVERT: D 57 ASP cc_start: 0.9132 (OUTLIER) cc_final: 0.8591 (m-30) REVERT: D 165 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7943 (mt-10) REVERT: D 368 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8290 (mp0) REVERT: D 429 CYS cc_start: 0.8805 (m) cc_final: 0.8523 (m) REVERT: D 444 CYS cc_start: 0.7956 (t) cc_final: 0.7372 (t) REVERT: D 515 MET cc_start: 0.8165 (mmm) cc_final: 0.7863 (mmt) REVERT: D 655 MET cc_start: 0.8364 (tpt) cc_final: 0.7860 (tpp) REVERT: D 681 LYS cc_start: 0.8372 (mtpt) cc_final: 0.7900 (mtpt) REVERT: D 694 MET cc_start: 0.8298 (mtp) cc_final: 0.8034 (mtt) REVERT: D 708 LEU cc_start: 0.8533 (tp) cc_final: 0.7902 (mt) REVERT: D 726 TYR cc_start: 0.8814 (t80) cc_final: 0.7998 (t80) REVERT: E 55 GLU cc_start: 0.8972 (tt0) cc_final: 0.8765 (pt0) REVERT: E 57 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8127 (m-30) REVERT: E 149 LYS cc_start: 0.8374 (tttt) cc_final: 0.7925 (tppt) REVERT: E 152 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8330 (tm-30) REVERT: E 323 GLN cc_start: 0.8416 (mt0) cc_final: 0.8158 (pt0) REVERT: E 388 GLN cc_start: 0.8493 (tp40) cc_final: 0.8115 (tp-100) REVERT: E 405 MET cc_start: 0.8938 (mtp) cc_final: 0.8622 (mtp) REVERT: E 423 ILE cc_start: 0.9561 (mt) cc_final: 0.9276 (mm) REVERT: E 431 GLU cc_start: 0.7483 (pm20) cc_final: 0.7242 (pm20) REVERT: E 433 VAL cc_start: 0.9147 (t) cc_final: 0.8946 (m) REVERT: E 434 GLU cc_start: 0.8104 (tt0) cc_final: 0.7870 (tm-30) REVERT: E 545 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8694 (m-30) REVERT: E 602 MET cc_start: 0.9042 (pmm) cc_final: 0.8718 (pmm) REVERT: E 694 MET cc_start: 0.8519 (mtp) cc_final: 0.8306 (mtt) REVERT: F 57 ASP cc_start: 0.8934 (OUTLIER) cc_final: 0.8598 (m-30) REVERT: F 81 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8224 (tp) REVERT: F 172 MET cc_start: 0.8642 (mmm) cc_final: 0.8431 (mmm) REVERT: F 233 ASP cc_start: 0.8578 (m-30) cc_final: 0.8007 (m-30) REVERT: F 307 ASP cc_start: 0.8339 (t0) cc_final: 0.8010 (t0) REVERT: F 416 ASN cc_start: 0.8049 (t0) cc_final: 0.7653 (t0) REVERT: F 431 GLU cc_start: 0.7705 (pm20) cc_final: 0.7477 (pm20) REVERT: F 515 MET cc_start: 0.7936 (mmt) cc_final: 0.7472 (mmt) REVERT: F 655 MET cc_start: 0.8325 (tpt) cc_final: 0.7979 (tpp) REVERT: F 677 LYS cc_start: 0.8085 (mttt) cc_final: 0.7214 (tptt) REVERT: F 681 LYS cc_start: 0.8467 (mtpt) cc_final: 0.8110 (mtpp) REVERT: F 698 ARG cc_start: 0.6653 (OUTLIER) cc_final: 0.6394 (ptt90) REVERT: F 708 LEU cc_start: 0.8248 (tp) cc_final: 0.7877 (mt) outliers start: 100 outliers final: 62 residues processed: 635 average time/residue: 0.2224 time to fit residues: 236.1046 Evaluate side-chains 571 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 500 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 625 TYR Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 643 LYS Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 533 GLU Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 533 GLU Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 534 THR Chi-restraints excluded: chain E residue 545 ASP Chi-restraints excluded: chain E residue 624 ILE Chi-restraints excluded: chain E residue 672 ILE Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 624 ILE Chi-restraints excluded: chain F residue 627 ARG Chi-restraints excluded: chain F residue 672 ILE Chi-restraints excluded: chain F residue 698 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 405 optimal weight: 0.0980 chunk 61 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 300 optimal weight: 0.0050 chunk 32 optimal weight: 6.9990 chunk 169 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 724 HIS ** E 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** F 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.109838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.097576 restraints weight = 77532.984| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.87 r_work: 0.3376 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 37068 Z= 0.110 Angle : 0.560 9.157 50310 Z= 0.287 Chirality : 0.044 0.165 5526 Planarity : 0.004 0.045 6336 Dihedral : 7.921 144.669 5124 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.95 % Allowed : 12.16 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.12), residues: 4458 helix: 0.45 (0.11), residues: 2232 sheet: -0.99 (0.29), residues: 246 loop : -0.95 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 698 TYR 0.017 0.001 TYR A 536 PHE 0.015 0.001 PHE A 519 TRP 0.012 0.001 TRP B 333 HIS 0.005 0.001 HIS D 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (37068) covalent geometry : angle 0.56050 / 0.29 (50310) hydrogen bonds : bond 0.03624 / 2.37 ( 1626) hydrogen bonds : angle 4.79779 / 3.37 ( 4644) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 597 time to evaluate : 1.371 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 21 ARG cc_start: 0.7532 (ttt180) cc_final: 0.6400 (mpt180) REVERT: A 23 GLN cc_start: 0.8360 (tt0) cc_final: 0.7908 (pt0) REVERT: A 41 MET cc_start: 0.8651 (ttp) cc_final: 0.8430 (ttp) REVERT: A 89 GLU cc_start: 0.8659 (tp30) cc_final: 0.8445 (tm-30) REVERT: A 149 LYS cc_start: 0.8174 (tttt) cc_final: 0.7966 (tppt) REVERT: A 307 ASP cc_start: 0.8224 (t0) cc_final: 0.7775 (t0) REVERT: A 360 ASP cc_start: 0.8368 (p0) cc_final: 0.7970 (p0) REVERT: A 362 VAL cc_start: 0.8340 (t) cc_final: 0.7920 (m) REVERT: A 416 ASN cc_start: 0.8003 (t0) cc_final: 0.7607 (t0) REVERT: A 674 ASP cc_start: 0.7484 (m-30) cc_final: 0.7119 (t0) REVERT: A 677 LYS cc_start: 0.7806 (mttt) cc_final: 0.7186 (tptt) REVERT: A 681 LYS cc_start: 0.8201 (mtpt) cc_final: 0.7619 (mtpt) REVERT: A 708 LEU cc_start: 0.8159 (tp) cc_final: 0.7836 (mp) REVERT: A 726 TYR cc_start: 0.8822 (t80) cc_final: 0.8200 (t80) REVERT: A 739 LEU cc_start: 0.8496 (tp) cc_final: 0.8253 (tp) REVERT: B 21 ARG cc_start: 0.7106 (ttt180) cc_final: 0.6314 (mmt-90) REVERT: B 89 GLU cc_start: 0.8829 (tp30) cc_final: 0.8542 (tm-30) REVERT: B 172 MET cc_start: 0.8385 (tpt) cc_final: 0.8017 (mmm) REVERT: B 190 TYR cc_start: 0.8625 (t80) cc_final: 0.8419 (t80) REVERT: B 253 SER cc_start: 0.9169 (m) cc_final: 0.8904 (t) REVERT: B 388 GLN cc_start: 0.8314 (tp40) cc_final: 0.7934 (tp-100) REVERT: B 405 MET cc_start: 0.8815 (mtp) cc_final: 0.8391 (mtp) REVERT: B 515 MET cc_start: 0.7631 (tpp) cc_final: 0.6486 (tpp) REVERT: B 517 TYR cc_start: 0.7720 (m-80) cc_final: 0.7075 (m-80) REVERT: B 545 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8450 (m-30) REVERT: B 602 MET cc_start: 0.8689 (pmm) cc_final: 0.8437 (pmm) REVERT: B 655 MET cc_start: 0.7183 (tpp) cc_final: 0.6600 (tpp) REVERT: B 677 LYS cc_start: 0.7845 (mttt) cc_final: 0.7170 (tptt) REVERT: B 694 MET cc_start: 0.8313 (mtp) cc_final: 0.8021 (mtt) REVERT: B 708 LEU cc_start: 0.8375 (tp) cc_final: 0.8170 (mp) REVERT: C 14 MET cc_start: 0.8443 (mpp) cc_final: 0.7565 (mpp) REVERT: C 21 ARG cc_start: 0.7397 (ttt180) cc_final: 0.6520 (mmt-90) REVERT: C 23 GLN cc_start: 0.8407 (tt0) cc_final: 0.7774 (pt0) REVERT: C 45 GLN cc_start: 0.8727 (tp40) cc_final: 0.8497 (tm-30) REVERT: C 57 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.7872 (m-30) REVERT: C 152 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8378 (tm-30) REVERT: C 313 ASP cc_start: 0.8191 (m-30) cc_final: 0.7741 (t0) REVERT: C 361 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8057 (tm-30) REVERT: C 368 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8185 (mt-10) REVERT: C 416 ASN cc_start: 0.7808 (t0) cc_final: 0.7564 (t0) REVERT: C 444 CYS cc_start: 0.7909 (t) cc_final: 0.7664 (t) REVERT: C 453 MET cc_start: 0.7686 (tpp) cc_final: 0.7396 (tpp) REVERT: C 515 MET cc_start: 0.8061 (mmm) cc_final: 0.7770 (mmt) REVERT: C 570 MET cc_start: 0.7489 (ttm) cc_final: 0.7262 (ttm) REVERT: C 654 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7477 (tm-30) REVERT: C 655 MET cc_start: 0.8458 (tpt) cc_final: 0.8235 (tpp) REVERT: C 681 LYS cc_start: 0.8379 (mtpt) cc_final: 0.7827 (mtpt) REVERT: C 694 MET cc_start: 0.8215 (mtp) cc_final: 0.7895 (mtt) REVERT: C 708 LEU cc_start: 0.8177 (tp) cc_final: 0.7612 (mp) REVERT: C 723 MET cc_start: 0.7735 (tpp) cc_final: 0.7195 (tpp) REVERT: C 726 TYR cc_start: 0.8793 (t80) cc_final: 0.8071 (t80) REVERT: D 23 GLN cc_start: 0.8373 (tt0) cc_final: 0.7721 (pt0) REVERT: D 313 ASP cc_start: 0.8220 (m-30) cc_final: 0.7849 (t0) REVERT: D 323 GLN cc_start: 0.8245 (mt0) cc_final: 0.7960 (pt0) REVERT: D 405 MET cc_start: 0.8855 (mtp) cc_final: 0.8629 (mtm) REVERT: D 416 ASN cc_start: 0.7909 (t0) cc_final: 0.7637 (t0) REVERT: D 429 CYS cc_start: 0.8789 (m) cc_final: 0.8493 (m) REVERT: D 453 MET cc_start: 0.7088 (mpp) cc_final: 0.6861 (mpp) REVERT: D 470 THR cc_start: 0.8682 (m) cc_final: 0.8388 (p) REVERT: D 515 MET cc_start: 0.8175 (mmm) cc_final: 0.7758 (mmt) REVERT: D 634 PHE cc_start: 0.6743 (p90) cc_final: 0.6460 (p90) REVERT: D 655 MET cc_start: 0.8386 (tpt) cc_final: 0.7770 (tpp) REVERT: D 681 LYS cc_start: 0.8378 (mtpt) cc_final: 0.7812 (mtpt) REVERT: D 694 MET cc_start: 0.8401 (mtp) cc_final: 0.8125 (mtt) REVERT: D 708 LEU cc_start: 0.8364 (tp) cc_final: 0.7732 (mp) REVERT: D 726 TYR cc_start: 0.8785 (t80) cc_final: 0.8202 (t80) REVERT: E 21 ARG cc_start: 0.7276 (ttt180) cc_final: 0.6269 (mmt-90) REVERT: E 89 GLU cc_start: 0.8812 (tp30) cc_final: 0.8549 (tm-30) REVERT: E 149 LYS cc_start: 0.8138 (tttt) cc_final: 0.7770 (tppt) REVERT: E 152 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8322 (tm-30) REVERT: E 190 TYR cc_start: 0.8622 (t80) cc_final: 0.8396 (t80) REVERT: E 323 GLN cc_start: 0.8349 (mt0) cc_final: 0.7969 (pt0) REVERT: E 388 GLN cc_start: 0.8461 (tp40) cc_final: 0.8040 (tp-100) REVERT: E 405 MET cc_start: 0.8825 (mtp) cc_final: 0.8428 (mtp) REVERT: E 427 ASN cc_start: 0.8596 (p0) cc_final: 0.8391 (p0) REVERT: E 431 GLU cc_start: 0.7412 (pm20) cc_final: 0.7110 (pm20) REVERT: E 433 VAL cc_start: 0.9164 (t) cc_final: 0.8870 (m) REVERT: E 461 TYR cc_start: 0.7713 (t80) cc_final: 0.7498 (t80) REVERT: E 515 MET cc_start: 0.7725 (tpp) cc_final: 0.6838 (tpp) REVERT: E 545 ASP cc_start: 0.8837 (OUTLIER) cc_final: 0.8631 (m-30) REVERT: E 602 MET cc_start: 0.8730 (pmm) cc_final: 0.8467 (pmm) REVERT: E 609 GLN cc_start: 0.8592 (tp-100) cc_final: 0.8299 (tp40) REVERT: E 627 ARG cc_start: 0.6482 (OUTLIER) cc_final: 0.6163 (mmp80) REVERT: E 674 ASP cc_start: 0.7488 (m-30) cc_final: 0.7108 (t0) REVERT: E 694 MET cc_start: 0.8333 (mtp) cc_final: 0.8049 (mtt) REVERT: F 81 ILE cc_start: 0.8625 (tt) cc_final: 0.8389 (tp) REVERT: F 89 GLU cc_start: 0.8688 (tp30) cc_final: 0.8421 (tm-30) REVERT: F 172 MET cc_start: 0.8530 (mmm) cc_final: 0.8298 (mmm) REVERT: F 362 VAL cc_start: 0.8572 (t) cc_final: 0.8198 (m) REVERT: F 416 ASN cc_start: 0.7896 (t0) cc_final: 0.7545 (t0) REVERT: F 515 MET cc_start: 0.7936 (mmt) cc_final: 0.7446 (mmt) REVERT: F 655 MET cc_start: 0.8348 (tpt) cc_final: 0.7984 (tpp) REVERT: F 674 ASP cc_start: 0.7388 (m-30) cc_final: 0.6966 (t0) REVERT: F 677 LYS cc_start: 0.7904 (mttt) cc_final: 0.7293 (tptt) REVERT: F 681 LYS cc_start: 0.8403 (mtpt) cc_final: 0.8005 (mtpp) REVERT: F 708 LEU cc_start: 0.8071 (tp) cc_final: 0.7796 (mp) REVERT: F 726 TYR cc_start: 0.8653 (t80) cc_final: 0.8041 (t80) outliers start: 76 outliers final: 43 residues processed: 650 average time/residue: 0.2244 time to fit residues: 243.4495 Evaluate side-chains 581 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 533 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 698 ARG Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 533 GLU Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain D residue 698 ARG Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 545 ASP Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 627 ARG Chi-restraints excluded: chain E residue 672 ILE Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 672 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 318 optimal weight: 8.9990 chunk 169 optimal weight: 6.9990 chunk 212 optimal weight: 4.9990 chunk 369 optimal weight: 6.9990 chunk 360 optimal weight: 3.9990 chunk 405 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 315 optimal weight: 5.9990 chunk 373 optimal weight: 0.8980 chunk 324 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 730 GLN D 214 GLN D 567 GLN ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.104147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.091868 restraints weight = 79066.804| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.84 r_work: 0.3280 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 37068 Z= 0.250 Angle : 0.655 9.107 50310 Z= 0.339 Chirality : 0.048 0.174 5526 Planarity : 0.004 0.045 6336 Dihedral : 8.184 157.239 5124 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.61 % Allowed : 13.13 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.13), residues: 4458 helix: 0.50 (0.11), residues: 2232 sheet: -0.82 (0.29), residues: 300 loop : -0.87 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 12 TYR 0.017 0.002 TYR E 190 PHE 0.020 0.002 PHE E 701 TRP 0.013 0.002 TRP A 333 HIS 0.006 0.001 HIS C 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.25 (37068) covalent geometry : angle 0.65477 / 0.34 (50310) hydrogen bonds : bond 0.04426 / 2.93 ( 1626) hydrogen bonds : angle 5.12873 / 3.60 ( 4644) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 518 time to evaluate : 1.543 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 23 GLN cc_start: 0.8352 (tt0) cc_final: 0.7941 (pt0) REVERT: A 57 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.8616 (m-30) REVERT: A 81 ILE cc_start: 0.8571 (tt) cc_final: 0.8269 (tp) REVERT: A 89 GLU cc_start: 0.8668 (tp30) cc_final: 0.8391 (tm-30) REVERT: A 131 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6865 (tp) REVERT: A 149 LYS cc_start: 0.8379 (tttt) cc_final: 0.8166 (tppt) REVERT: A 233 ASP cc_start: 0.8512 (m-30) cc_final: 0.7976 (m-30) REVERT: A 307 ASP cc_start: 0.8300 (t0) cc_final: 0.7994 (t0) REVERT: A 416 ASN cc_start: 0.8178 (t0) cc_final: 0.7637 (t0) REVERT: A 677 LYS cc_start: 0.7966 (mttt) cc_final: 0.7175 (tptt) REVERT: A 681 LYS cc_start: 0.8333 (mtpt) cc_final: 0.7951 (mtpp) REVERT: A 708 LEU cc_start: 0.8276 (tp) cc_final: 0.7976 (mp) REVERT: A 739 LEU cc_start: 0.8634 (tp) cc_final: 0.8412 (tp) REVERT: B 21 ARG cc_start: 0.7443 (ttt180) cc_final: 0.6527 (mmt-90) REVERT: B 57 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8059 (m-30) REVERT: B 89 GLU cc_start: 0.8728 (tp30) cc_final: 0.8397 (tm-30) REVERT: B 172 MET cc_start: 0.8597 (tpt) cc_final: 0.8382 (mmm) REVERT: B 253 SER cc_start: 0.9197 (m) cc_final: 0.8906 (t) REVERT: B 320 LYS cc_start: 0.8709 (mtpt) cc_final: 0.8442 (mtmt) REVERT: B 405 MET cc_start: 0.8920 (mtp) cc_final: 0.8660 (mtp) REVERT: B 431 GLU cc_start: 0.7578 (pm20) cc_final: 0.7281 (pm20) REVERT: B 433 VAL cc_start: 0.9202 (t) cc_final: 0.8909 (m) REVERT: B 545 ASP cc_start: 0.8831 (OUTLIER) cc_final: 0.8555 (m-30) REVERT: B 628 ARG cc_start: 0.6889 (OUTLIER) cc_final: 0.6576 (tpm170) REVERT: B 677 LYS cc_start: 0.7378 (mttt) cc_final: 0.7114 (tptt) REVERT: B 694 MET cc_start: 0.8281 (mtp) cc_final: 0.8030 (mtt) REVERT: B 708 LEU cc_start: 0.8382 (tp) cc_final: 0.8081 (mp) REVERT: C 14 MET cc_start: 0.8579 (mpp) cc_final: 0.8200 (mpp) REVERT: C 23 GLN cc_start: 0.8283 (tt0) cc_final: 0.7831 (pt0) REVERT: C 57 ASP cc_start: 0.8824 (OUTLIER) cc_final: 0.8476 (m-30) REVERT: C 189 THR cc_start: 0.9226 (OUTLIER) cc_final: 0.8934 (p) REVERT: C 233 ASP cc_start: 0.8593 (m-30) cc_final: 0.7948 (m-30) REVERT: C 313 ASP cc_start: 0.8349 (m-30) cc_final: 0.7868 (t0) REVERT: C 388 GLN cc_start: 0.8833 (tp-100) cc_final: 0.8444 (tp-100) REVERT: C 416 ASN cc_start: 0.8118 (t0) cc_final: 0.7855 (t0) REVERT: C 431 GLU cc_start: 0.7683 (pm20) cc_final: 0.7404 (pm20) REVERT: C 444 CYS cc_start: 0.8067 (t) cc_final: 0.7774 (t) REVERT: C 453 MET cc_start: 0.8004 (tpp) cc_final: 0.7598 (tpp) REVERT: C 515 MET cc_start: 0.8132 (mmm) cc_final: 0.7917 (mmt) REVERT: C 627 ARG cc_start: 0.6411 (OUTLIER) cc_final: 0.5632 (mmp80) REVERT: C 655 MET cc_start: 0.8562 (tpt) cc_final: 0.8309 (tpp) REVERT: C 681 LYS cc_start: 0.8309 (mtpt) cc_final: 0.7721 (mtpt) REVERT: C 694 MET cc_start: 0.8294 (mtp) cc_final: 0.7870 (mtt) REVERT: C 708 LEU cc_start: 0.8395 (tp) cc_final: 0.7843 (mp) REVERT: C 726 TYR cc_start: 0.8837 (t80) cc_final: 0.8280 (t80) REVERT: D 23 GLN cc_start: 0.8296 (tt0) cc_final: 0.7778 (pt0) REVERT: D 313 ASP cc_start: 0.8313 (m-30) cc_final: 0.7953 (t0) REVERT: D 323 GLN cc_start: 0.8416 (mt0) cc_final: 0.8089 (pt0) REVERT: D 388 GLN cc_start: 0.8716 (tp-100) cc_final: 0.8366 (tp-100) REVERT: D 416 ASN cc_start: 0.8017 (t0) cc_final: 0.7749 (t0) REVERT: D 429 CYS cc_start: 0.8886 (m) cc_final: 0.8558 (m) REVERT: D 434 GLU cc_start: 0.7310 (tm-30) cc_final: 0.7042 (tm-30) REVERT: D 515 MET cc_start: 0.8233 (mmm) cc_final: 0.7975 (mmt) REVERT: D 634 PHE cc_start: 0.6843 (p90) cc_final: 0.6566 (p90) REVERT: D 655 MET cc_start: 0.8374 (tpt) cc_final: 0.7896 (tpp) REVERT: D 657 ASN cc_start: 0.8969 (t0) cc_final: 0.8768 (t0) REVERT: D 681 LYS cc_start: 0.8391 (mtpt) cc_final: 0.7820 (mtpt) REVERT: D 685 GLU cc_start: 0.8279 (mp0) cc_final: 0.7906 (mp0) REVERT: D 694 MET cc_start: 0.8233 (mtp) cc_final: 0.7853 (mtt) REVERT: D 708 LEU cc_start: 0.8306 (tp) cc_final: 0.7787 (mp) REVERT: D 726 TYR cc_start: 0.8786 (t80) cc_final: 0.8276 (t80) REVERT: D 742 ARG cc_start: 0.7235 (ptt180) cc_final: 0.7031 (ptt90) REVERT: E 57 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8388 (m-30) REVERT: E 89 GLU cc_start: 0.8729 (tp30) cc_final: 0.8437 (tm-30) REVERT: E 149 LYS cc_start: 0.8299 (tttt) cc_final: 0.7910 (tppt) REVERT: E 152 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8104 (tm-30) REVERT: E 172 MET cc_start: 0.8359 (mmm) cc_final: 0.7967 (mmm) REVERT: E 190 TYR cc_start: 0.8740 (t80) cc_final: 0.8530 (t80) REVERT: E 323 GLN cc_start: 0.8561 (mt0) cc_final: 0.8217 (pt0) REVERT: E 405 MET cc_start: 0.8892 (mtp) cc_final: 0.8604 (mtp) REVERT: E 431 GLU cc_start: 0.7476 (pm20) cc_final: 0.7214 (pm20) REVERT: E 515 MET cc_start: 0.7825 (tpp) cc_final: 0.7059 (tpp) REVERT: E 545 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8606 (m-30) REVERT: E 627 ARG cc_start: 0.6626 (OUTLIER) cc_final: 0.6222 (mmp80) REVERT: E 694 MET cc_start: 0.8441 (mtp) cc_final: 0.8167 (mtt) REVERT: F 81 ILE cc_start: 0.8737 (tt) cc_final: 0.8524 (tp) REVERT: F 89 GLU cc_start: 0.8734 (tp30) cc_final: 0.8415 (tm-30) REVERT: F 131 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6790 (tt) REVERT: F 233 ASP cc_start: 0.8492 (m-30) cc_final: 0.7957 (m-30) REVERT: F 416 ASN cc_start: 0.8063 (t0) cc_final: 0.7561 (t0) REVERT: F 515 MET cc_start: 0.7982 (mmt) cc_final: 0.7534 (mmt) REVERT: F 655 MET cc_start: 0.8351 (tpt) cc_final: 0.7956 (tpp) REVERT: F 677 LYS cc_start: 0.8044 (mttt) cc_final: 0.7247 (tptt) REVERT: F 681 LYS cc_start: 0.8288 (mtpt) cc_final: 0.7951 (mtpp) REVERT: F 708 LEU cc_start: 0.8201 (tp) cc_final: 0.7908 (mp) outliers start: 102 outliers final: 69 residues processed: 589 average time/residue: 0.2251 time to fit residues: 220.9692 Evaluate side-chains 575 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 494 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 625 TYR Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 628 ARG Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 534 THR Chi-restraints excluded: chain E residue 545 ASP Chi-restraints excluded: chain E residue 569 ASP Chi-restraints excluded: chain E residue 627 ARG Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 534 THR Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 624 ILE Chi-restraints excluded: chain F residue 627 ARG Chi-restraints excluded: chain F residue 672 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 379 optimal weight: 5.9990 chunk 228 optimal weight: 0.8980 chunk 275 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 428 optimal weight: 4.9990 chunk 236 optimal weight: 4.9990 chunk 375 optimal weight: 0.7980 chunk 283 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 358 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 567 GLN E 38 GLN E 214 GLN ** E 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.106840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.094114 restraints weight = 79541.956| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.93 r_work: 0.3315 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 37068 Z= 0.163 Angle : 0.585 8.782 50310 Z= 0.300 Chirality : 0.045 0.184 5526 Planarity : 0.004 0.045 6336 Dihedral : 7.916 157.638 5124 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.59 % Allowed : 13.42 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.13), residues: 4458 helix: 0.79 (0.11), residues: 2220 sheet: -0.80 (0.30), residues: 300 loop : -0.76 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 12 TYR 0.015 0.001 TYR E 726 PHE 0.015 0.002 PHE E 701 TRP 0.014 0.001 TRP B 333 HIS 0.004 0.001 HIS F 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (37068) covalent geometry : angle 0.58517 / 0.30 (50310) hydrogen bonds : bond 0.03824 / 2.53 ( 1626) hydrogen bonds : angle 4.84849 / 3.41 ( 4644) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 533 time to evaluate : 1.408 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 21 ARG cc_start: 0.7443 (ttt180) cc_final: 0.6454 (mpt180) REVERT: A 23 GLN cc_start: 0.8315 (tt0) cc_final: 0.7907 (pt0) REVERT: A 57 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.8327 (m-30) REVERT: A 81 ILE cc_start: 0.8709 (tt) cc_final: 0.8484 (tp) REVERT: A 89 GLU cc_start: 0.8732 (tp30) cc_final: 0.8386 (tm-30) REVERT: A 115 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8795 (mtm) REVERT: A 149 LYS cc_start: 0.8307 (tttt) cc_final: 0.8095 (tppt) REVERT: A 189 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8919 (p) REVERT: A 307 ASP cc_start: 0.8184 (t0) cc_final: 0.7835 (t0) REVERT: A 327 ASP cc_start: 0.8722 (t0) cc_final: 0.8060 (t0) REVERT: A 416 ASN cc_start: 0.8155 (t0) cc_final: 0.7622 (t0) REVERT: A 515 MET cc_start: 0.8025 (tpp) cc_final: 0.7256 (tpp) REVERT: A 677 LYS cc_start: 0.7912 (mttt) cc_final: 0.7193 (tptt) REVERT: A 681 LYS cc_start: 0.8457 (mtpt) cc_final: 0.8049 (mtpp) REVERT: A 708 LEU cc_start: 0.8203 (tp) cc_final: 0.7905 (mt) REVERT: B 12 ARG cc_start: 0.6539 (mmt180) cc_final: 0.6241 (mmt180) REVERT: B 21 ARG cc_start: 0.7668 (ttt180) cc_final: 0.6696 (mmt-90) REVERT: B 57 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8266 (m-30) REVERT: B 89 GLU cc_start: 0.8795 (tp30) cc_final: 0.8566 (tm-30) REVERT: B 172 MET cc_start: 0.8545 (tpt) cc_final: 0.8197 (mmm) REVERT: B 253 SER cc_start: 0.9121 (m) cc_final: 0.8836 (t) REVERT: B 320 LYS cc_start: 0.8691 (mtpt) cc_final: 0.8439 (mtmt) REVERT: B 405 MET cc_start: 0.8877 (mtp) cc_final: 0.8579 (mtp) REVERT: B 431 GLU cc_start: 0.7577 (pm20) cc_final: 0.7307 (pm20) REVERT: B 433 VAL cc_start: 0.9199 (t) cc_final: 0.8939 (m) REVERT: B 515 MET cc_start: 0.7741 (tpp) cc_final: 0.6902 (tpp) REVERT: B 545 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8538 (m-30) REVERT: B 677 LYS cc_start: 0.7740 (mttt) cc_final: 0.7243 (tptt) REVERT: B 694 MET cc_start: 0.8206 (mtp) cc_final: 0.7953 (mtt) REVERT: B 708 LEU cc_start: 0.8391 (tp) cc_final: 0.8091 (mp) REVERT: C 14 MET cc_start: 0.8538 (mpp) cc_final: 0.8156 (mpp) REVERT: C 21 ARG cc_start: 0.7733 (ttt180) cc_final: 0.6613 (mmt180) REVERT: C 23 GLN cc_start: 0.8339 (tt0) cc_final: 0.7921 (pt0) REVERT: C 57 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8109 (m-30) REVERT: C 313 ASP cc_start: 0.8258 (m-30) cc_final: 0.7882 (t0) REVERT: C 327 ASP cc_start: 0.8449 (m-30) cc_final: 0.8153 (t0) REVERT: C 388 GLN cc_start: 0.8780 (tp-100) cc_final: 0.8387 (tp-100) REVERT: C 416 ASN cc_start: 0.8093 (t0) cc_final: 0.7766 (t0) REVERT: C 431 GLU cc_start: 0.7661 (pm20) cc_final: 0.7367 (pm20) REVERT: C 444 CYS cc_start: 0.8142 (t) cc_final: 0.7909 (t) REVERT: C 453 MET cc_start: 0.8008 (tpp) cc_final: 0.7764 (tpp) REVERT: C 515 MET cc_start: 0.8116 (mmm) cc_final: 0.7905 (mmt) REVERT: C 546 LEU cc_start: 0.9248 (mt) cc_final: 0.8962 (mt) REVERT: C 627 ARG cc_start: 0.6600 (OUTLIER) cc_final: 0.5827 (mmp80) REVERT: C 654 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7689 (tm-30) REVERT: C 655 MET cc_start: 0.8442 (tpt) cc_final: 0.8177 (tpp) REVERT: C 680 TYR cc_start: 0.8419 (m-80) cc_final: 0.8195 (m-80) REVERT: C 681 LYS cc_start: 0.8348 (mtpt) cc_final: 0.7692 (mtpt) REVERT: C 694 MET cc_start: 0.8206 (mtp) cc_final: 0.7770 (mtt) REVERT: C 708 LEU cc_start: 0.8249 (tp) cc_final: 0.7718 (mp) REVERT: C 726 TYR cc_start: 0.8832 (t80) cc_final: 0.8321 (t80) REVERT: D 23 GLN cc_start: 0.8222 (tt0) cc_final: 0.7767 (pt0) REVERT: D 89 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8205 (tm-30) REVERT: D 313 ASP cc_start: 0.8284 (m-30) cc_final: 0.7935 (t0) REVERT: D 323 GLN cc_start: 0.8418 (mt0) cc_final: 0.8101 (pt0) REVERT: D 361 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8076 (tm-30) REVERT: D 416 ASN cc_start: 0.8049 (t0) cc_final: 0.7663 (t0) REVERT: D 429 CYS cc_start: 0.8846 (m) cc_final: 0.8634 (p) REVERT: D 434 GLU cc_start: 0.7248 (tm-30) cc_final: 0.7022 (tm-30) REVERT: D 515 MET cc_start: 0.8219 (mmm) cc_final: 0.7854 (mmt) REVERT: D 627 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.5964 (mmp80) REVERT: D 634 PHE cc_start: 0.6775 (p90) cc_final: 0.6515 (p90) REVERT: D 655 MET cc_start: 0.8319 (tpt) cc_final: 0.7867 (tpp) REVERT: D 681 LYS cc_start: 0.8298 (mtpt) cc_final: 0.7609 (mtpt) REVERT: D 694 MET cc_start: 0.8166 (mtp) cc_final: 0.7865 (mtt) REVERT: D 708 LEU cc_start: 0.8316 (tp) cc_final: 0.7788 (mp) REVERT: E 31 MET cc_start: 0.8368 (mmt) cc_final: 0.7889 (mmt) REVERT: E 57 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8356 (m-30) REVERT: E 89 GLU cc_start: 0.8773 (tp30) cc_final: 0.8556 (tm-30) REVERT: E 149 LYS cc_start: 0.8261 (tttt) cc_final: 0.7933 (tppt) REVERT: E 152 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8153 (tm-30) REVERT: E 172 MET cc_start: 0.8306 (mmm) cc_final: 0.7986 (mmm) REVERT: E 323 GLN cc_start: 0.8577 (mt0) cc_final: 0.8273 (pt0) REVERT: E 366 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8265 (mp0) REVERT: E 405 MET cc_start: 0.8835 (mtp) cc_final: 0.8551 (mtp) REVERT: E 431 GLU cc_start: 0.7469 (pm20) cc_final: 0.7179 (pm20) REVERT: E 434 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7191 (tm-30) REVERT: E 515 MET cc_start: 0.7772 (tpp) cc_final: 0.7009 (tpp) REVERT: E 545 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.8564 (m-30) REVERT: E 602 MET cc_start: 0.8687 (pmm) cc_final: 0.8450 (pmm) REVERT: E 627 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6404 (mmp80) REVERT: E 694 MET cc_start: 0.8347 (mtp) cc_final: 0.8089 (mtt) REVERT: F 81 ILE cc_start: 0.8738 (tt) cc_final: 0.8533 (tp) REVERT: F 89 GLU cc_start: 0.8729 (tp30) cc_final: 0.8499 (tm-30) REVERT: F 115 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8801 (mtm) REVERT: F 416 ASN cc_start: 0.8054 (t0) cc_final: 0.7546 (t0) REVERT: F 515 MET cc_start: 0.8020 (mmt) cc_final: 0.7604 (mmt) REVERT: F 655 MET cc_start: 0.8379 (tpt) cc_final: 0.7979 (tpp) REVERT: F 674 ASP cc_start: 0.7474 (m-30) cc_final: 0.7018 (t0) REVERT: F 677 LYS cc_start: 0.7968 (mttt) cc_final: 0.7206 (tptt) REVERT: F 681 LYS cc_start: 0.8297 (mtpt) cc_final: 0.7966 (mtpp) REVERT: F 708 LEU cc_start: 0.8148 (tp) cc_final: 0.7848 (mp) outliers start: 101 outliers final: 63 residues processed: 608 average time/residue: 0.2234 time to fit residues: 225.5207 Evaluate side-chains 574 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 497 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 628 ARG Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 627 ARG Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 533 GLU Chi-restraints excluded: chain E residue 534 THR Chi-restraints excluded: chain E residue 545 ASP Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 627 ARG Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 624 ILE Chi-restraints excluded: chain F residue 627 ARG Chi-restraints excluded: chain F residue 672 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 118 optimal weight: 2.9990 chunk 402 optimal weight: 0.9990 chunk 193 optimal weight: 7.9990 chunk 300 optimal weight: 0.9990 chunk 333 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 311 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 225 optimal weight: 7.9990 chunk 247 optimal weight: 4.9990 chunk 407 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN C 388 GLN D 724 HIS ** E 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 GLN ** F 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.106726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.093962 restraints weight = 79401.543| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.92 r_work: 0.3311 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 37068 Z= 0.166 Angle : 0.591 8.895 50310 Z= 0.303 Chirality : 0.045 0.173 5526 Planarity : 0.004 0.041 6336 Dihedral : 7.753 161.828 5124 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.56 % Allowed : 13.93 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.13), residues: 4458 helix: 0.90 (0.11), residues: 2220 sheet: -0.78 (0.30), residues: 300 loop : -0.72 (0.15), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 742 TYR 0.036 0.001 TYR E 190 PHE 0.015 0.002 PHE E 94 TRP 0.012 0.001 TRP B 333 HIS 0.007 0.001 HIS D 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (37068) covalent geometry : angle 0.59062 / 0.30 (50310) hydrogen bonds : bond 0.03845 / 2.55 ( 1626) hydrogen bonds : angle 4.83077 / 3.40 ( 4644) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 531 time to evaluate : 1.104 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 21 ARG cc_start: 0.7527 (ttt180) cc_final: 0.6488 (mpt180) REVERT: A 23 GLN cc_start: 0.8312 (tt0) cc_final: 0.7948 (pt0) REVERT: A 57 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8265 (m-30) REVERT: A 89 GLU cc_start: 0.8774 (tp30) cc_final: 0.8436 (tm-30) REVERT: A 149 LYS cc_start: 0.8368 (tttt) cc_final: 0.8167 (tppt) REVERT: A 307 ASP cc_start: 0.8325 (t0) cc_final: 0.7949 (t0) REVERT: A 327 ASP cc_start: 0.8730 (t0) cc_final: 0.8066 (t0) REVERT: A 416 ASN cc_start: 0.8154 (t0) cc_final: 0.7620 (t0) REVERT: A 515 MET cc_start: 0.8043 (tpp) cc_final: 0.7314 (tpp) REVERT: A 655 MET cc_start: 0.7690 (tpp) cc_final: 0.7342 (tpp) REVERT: A 677 LYS cc_start: 0.7880 (mttt) cc_final: 0.7185 (tptt) REVERT: A 681 LYS cc_start: 0.8464 (mtpt) cc_final: 0.8048 (mtpp) REVERT: A 708 LEU cc_start: 0.8290 (tp) cc_final: 0.7975 (mt) REVERT: B 21 ARG cc_start: 0.7708 (ttt180) cc_final: 0.6712 (mmt-90) REVERT: B 57 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8329 (m-30) REVERT: B 89 GLU cc_start: 0.8836 (tp30) cc_final: 0.8507 (tm-30) REVERT: B 172 MET cc_start: 0.8455 (tpt) cc_final: 0.8249 (mmm) REVERT: B 253 SER cc_start: 0.9126 (m) cc_final: 0.8813 (t) REVERT: B 351 MET cc_start: 0.8217 (ptp) cc_final: 0.7794 (mtm) REVERT: B 405 MET cc_start: 0.8861 (mtp) cc_final: 0.8579 (mtp) REVERT: B 431 GLU cc_start: 0.7576 (pm20) cc_final: 0.7284 (pm20) REVERT: B 433 VAL cc_start: 0.9197 (t) cc_final: 0.8953 (m) REVERT: B 545 ASP cc_start: 0.8799 (OUTLIER) cc_final: 0.8510 (m-30) REVERT: B 602 MET cc_start: 0.8667 (pmm) cc_final: 0.8456 (pmm) REVERT: B 694 MET cc_start: 0.8327 (mtp) cc_final: 0.8064 (mtt) REVERT: B 705 SER cc_start: 0.8564 (t) cc_final: 0.8264 (t) REVERT: B 708 LEU cc_start: 0.8410 (tp) cc_final: 0.8071 (mp) REVERT: C 14 MET cc_start: 0.8458 (mpp) cc_final: 0.8075 (mpp) REVERT: C 21 ARG cc_start: 0.7787 (ttt180) cc_final: 0.6674 (mmt180) REVERT: C 23 GLN cc_start: 0.8325 (tt0) cc_final: 0.7795 (pt0) REVERT: C 313 ASP cc_start: 0.8308 (m-30) cc_final: 0.7884 (t0) REVERT: C 327 ASP cc_start: 0.8441 (m-30) cc_final: 0.8149 (t0) REVERT: C 339 MET cc_start: 0.8093 (ttp) cc_final: 0.7752 (ttp) REVERT: C 416 ASN cc_start: 0.8103 (t0) cc_final: 0.7797 (t0) REVERT: C 431 GLU cc_start: 0.7613 (pm20) cc_final: 0.7399 (pm20) REVERT: C 444 CYS cc_start: 0.8190 (t) cc_final: 0.7933 (t) REVERT: C 453 MET cc_start: 0.8022 (tpp) cc_final: 0.7768 (tpp) REVERT: C 515 MET cc_start: 0.8129 (mmm) cc_final: 0.7915 (mmt) REVERT: C 546 LEU cc_start: 0.9252 (mt) cc_final: 0.8972 (mt) REVERT: C 627 ARG cc_start: 0.6426 (OUTLIER) cc_final: 0.5588 (mmp80) REVERT: C 654 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: C 655 MET cc_start: 0.8423 (tpt) cc_final: 0.8159 (tpp) REVERT: C 681 LYS cc_start: 0.8279 (mtpt) cc_final: 0.7600 (mtpt) REVERT: C 694 MET cc_start: 0.8197 (mtp) cc_final: 0.7782 (mtt) REVERT: C 708 LEU cc_start: 0.8321 (tp) cc_final: 0.7766 (mp) REVERT: C 726 TYR cc_start: 0.8830 (t80) cc_final: 0.8292 (t80) REVERT: D 23 GLN cc_start: 0.8250 (tt0) cc_final: 0.7820 (pt0) REVERT: D 313 ASP cc_start: 0.8283 (m-30) cc_final: 0.7933 (t0) REVERT: D 323 GLN cc_start: 0.8433 (mt0) cc_final: 0.8118 (pt0) REVERT: D 361 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8091 (tm-30) REVERT: D 388 GLN cc_start: 0.8696 (tp-100) cc_final: 0.8442 (tp-100) REVERT: D 416 ASN cc_start: 0.8023 (t0) cc_final: 0.7658 (t0) REVERT: D 429 CYS cc_start: 0.8779 (m) cc_final: 0.8557 (p) REVERT: D 515 MET cc_start: 0.8185 (mmm) cc_final: 0.7854 (mmt) REVERT: D 627 ARG cc_start: 0.6672 (OUTLIER) cc_final: 0.5774 (mmp80) REVERT: D 655 MET cc_start: 0.8316 (tpt) cc_final: 0.8051 (tpp) REVERT: D 694 MET cc_start: 0.8127 (mtp) cc_final: 0.7799 (mtt) REVERT: D 708 LEU cc_start: 0.8333 (tp) cc_final: 0.7816 (mp) REVERT: E 31 MET cc_start: 0.8409 (mmt) cc_final: 0.7979 (mmt) REVERT: E 89 GLU cc_start: 0.8831 (tp30) cc_final: 0.8490 (tm-30) REVERT: E 149 LYS cc_start: 0.8251 (tttt) cc_final: 0.7917 (tppt) REVERT: E 152 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8008 (tm-30) REVERT: E 190 TYR cc_start: 0.8580 (t80) cc_final: 0.8338 (t80) REVERT: E 323 GLN cc_start: 0.8575 (mt0) cc_final: 0.8275 (pt0) REVERT: E 405 MET cc_start: 0.8840 (mtp) cc_final: 0.8557 (mtp) REVERT: E 431 GLU cc_start: 0.7549 (pm20) cc_final: 0.7196 (pm20) REVERT: E 434 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7216 (tm-30) REVERT: E 545 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8551 (m-30) REVERT: E 627 ARG cc_start: 0.6533 (OUTLIER) cc_final: 0.6052 (mmp80) REVERT: E 694 MET cc_start: 0.8341 (mtp) cc_final: 0.8054 (mtt) REVERT: F 81 ILE cc_start: 0.8734 (tt) cc_final: 0.8532 (tp) REVERT: F 233 ASP cc_start: 0.8496 (m-30) cc_final: 0.7952 (m-30) REVERT: F 310 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8154 (tp30) REVERT: F 416 ASN cc_start: 0.8060 (t0) cc_final: 0.7538 (t0) REVERT: F 515 MET cc_start: 0.8029 (mmt) cc_final: 0.7625 (mmt) REVERT: F 655 MET cc_start: 0.8371 (tpt) cc_final: 0.7966 (tpp) REVERT: F 674 ASP cc_start: 0.7475 (m-30) cc_final: 0.7037 (t0) REVERT: F 677 LYS cc_start: 0.7951 (mttt) cc_final: 0.7203 (tptt) REVERT: F 681 LYS cc_start: 0.8305 (mtpt) cc_final: 0.7975 (mtpp) REVERT: F 708 LEU cc_start: 0.8146 (tp) cc_final: 0.7842 (mp) REVERT: F 726 TYR cc_start: 0.8573 (t80) cc_final: 0.8338 (t80) outliers start: 100 outliers final: 63 residues processed: 606 average time/residue: 0.2111 time to fit residues: 212.4254 Evaluate side-chains 565 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 494 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 628 ARG Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 627 ARG Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 533 GLU Chi-restraints excluded: chain E residue 534 THR Chi-restraints excluded: chain E residue 545 ASP Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 627 ARG Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 627 ARG Chi-restraints excluded: chain F residue 672 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 1 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 432 optimal weight: 0.9980 chunk 116 optimal weight: 8.9990 chunk 184 optimal weight: 0.0170 chunk 411 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 375 optimal weight: 5.9990 chunk 339 optimal weight: 7.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 GLN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.107738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.095503 restraints weight = 77874.255| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.84 r_work: 0.3343 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 37068 Z= 0.132 Angle : 0.583 10.762 50310 Z= 0.295 Chirality : 0.044 0.221 5526 Planarity : 0.003 0.041 6336 Dihedral : 7.384 159.644 5124 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.18 % Allowed : 14.67 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.13), residues: 4458 helix: 1.00 (0.11), residues: 2220 sheet: -0.87 (0.30), residues: 306 loop : -0.61 (0.15), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 698 TYR 0.026 0.001 TYR E 190 PHE 0.012 0.002 PHE B 94 TRP 0.028 0.001 TRP A 728 HIS 0.004 0.001 HIS A 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (37068) covalent geometry : angle 0.58250 / 0.29 (50310) hydrogen bonds : bond 0.03583 / 2.36 ( 1626) hydrogen bonds : angle 4.67430 / 3.29 ( 4644) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 542 time to evaluate : 1.256 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 21 ARG cc_start: 0.7410 (ttt180) cc_final: 0.6552 (mpt180) REVERT: A 26 CYS cc_start: 0.8077 (m) cc_final: 0.7793 (m) REVERT: A 89 GLU cc_start: 0.8800 (tp30) cc_final: 0.8437 (tm-30) REVERT: A 149 LYS cc_start: 0.8267 (tttt) cc_final: 0.8064 (tppt) REVERT: A 307 ASP cc_start: 0.8352 (t0) cc_final: 0.7818 (t0) REVERT: A 327 ASP cc_start: 0.8718 (t0) cc_final: 0.8084 (t0) REVERT: A 416 ASN cc_start: 0.8130 (t0) cc_final: 0.7579 (t0) REVERT: A 515 MET cc_start: 0.8061 (tpp) cc_final: 0.7340 (tpp) REVERT: A 674 ASP cc_start: 0.7501 (m-30) cc_final: 0.7246 (t0) REVERT: A 677 LYS cc_start: 0.7895 (mttt) cc_final: 0.7245 (tptt) REVERT: A 681 LYS cc_start: 0.8383 (mtpt) cc_final: 0.7971 (mtpp) REVERT: A 708 LEU cc_start: 0.8184 (tp) cc_final: 0.7869 (mt) REVERT: B 21 ARG cc_start: 0.7684 (ttt180) cc_final: 0.6731 (mmt-90) REVERT: B 89 GLU cc_start: 0.8868 (tp30) cc_final: 0.8467 (tm-30) REVERT: B 253 SER cc_start: 0.9096 (m) cc_final: 0.8790 (t) REVERT: B 320 LYS cc_start: 0.8602 (mtpt) cc_final: 0.8292 (mtmt) REVERT: B 323 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8155 (pm20) REVERT: B 405 MET cc_start: 0.8837 (mtp) cc_final: 0.8537 (mtp) REVERT: B 433 VAL cc_start: 0.9138 (t) cc_final: 0.8886 (m) REVERT: B 545 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8484 (m-30) REVERT: B 609 GLN cc_start: 0.8647 (tp-100) cc_final: 0.8340 (tp40) REVERT: B 694 MET cc_start: 0.8312 (mtp) cc_final: 0.8013 (mtt) REVERT: B 705 SER cc_start: 0.8532 (t) cc_final: 0.8210 (t) REVERT: B 708 LEU cc_start: 0.8381 (tp) cc_final: 0.8042 (mp) REVERT: C 14 MET cc_start: 0.8469 (mpp) cc_final: 0.8064 (mpp) REVERT: C 21 ARG cc_start: 0.7764 (ttt180) cc_final: 0.6750 (mpt180) REVERT: C 23 GLN cc_start: 0.8339 (tt0) cc_final: 0.7783 (pt0) REVERT: C 45 GLN cc_start: 0.8770 (tp40) cc_final: 0.8556 (tm-30) REVERT: C 57 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.7948 (m-30) REVERT: C 313 ASP cc_start: 0.8273 (m-30) cc_final: 0.7845 (t0) REVERT: C 327 ASP cc_start: 0.8456 (m-30) cc_final: 0.8185 (t0) REVERT: C 416 ASN cc_start: 0.8112 (t0) cc_final: 0.7755 (t0) REVERT: C 431 GLU cc_start: 0.7626 (pm20) cc_final: 0.7342 (pm20) REVERT: C 444 CYS cc_start: 0.8114 (t) cc_final: 0.7906 (t) REVERT: C 453 MET cc_start: 0.7963 (tpp) cc_final: 0.7708 (tpp) REVERT: C 515 MET cc_start: 0.8080 (mmm) cc_final: 0.7803 (mmt) REVERT: C 546 LEU cc_start: 0.9252 (mt) cc_final: 0.8971 (mt) REVERT: C 627 ARG cc_start: 0.6415 (OUTLIER) cc_final: 0.5580 (mmp80) REVERT: C 655 MET cc_start: 0.8445 (tpt) cc_final: 0.8035 (tpp) REVERT: C 681 LYS cc_start: 0.8346 (mtpt) cc_final: 0.7647 (mtpt) REVERT: C 694 MET cc_start: 0.8182 (mtp) cc_final: 0.7787 (mtt) REVERT: C 708 LEU cc_start: 0.8267 (tp) cc_final: 0.7730 (mp) REVERT: C 726 TYR cc_start: 0.8810 (t80) cc_final: 0.8355 (t80) REVERT: D 23 GLN cc_start: 0.8209 (tt0) cc_final: 0.7798 (pt0) REVERT: D 307 ASP cc_start: 0.8290 (m-30) cc_final: 0.8008 (t0) REVERT: D 323 GLN cc_start: 0.8417 (mt0) cc_final: 0.8097 (pt0) REVERT: D 361 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8109 (tm-30) REVERT: D 388 GLN cc_start: 0.8642 (tp-100) cc_final: 0.8296 (tp-100) REVERT: D 416 ASN cc_start: 0.8018 (t0) cc_final: 0.7634 (t0) REVERT: D 429 CYS cc_start: 0.8775 (m) cc_final: 0.8507 (p) REVERT: D 438 LYS cc_start: 0.8967 (mptt) cc_final: 0.8714 (tmmt) REVERT: D 627 ARG cc_start: 0.6590 (OUTLIER) cc_final: 0.5815 (mmp80) REVERT: D 655 MET cc_start: 0.8315 (tpt) cc_final: 0.8022 (tpp) REVERT: D 681 LYS cc_start: 0.8003 (mtpt) cc_final: 0.7318 (mtpt) REVERT: D 694 MET cc_start: 0.8096 (mtp) cc_final: 0.7770 (mtt) REVERT: D 708 LEU cc_start: 0.8282 (tp) cc_final: 0.7742 (mp) REVERT: E 12 ARG cc_start: 0.6566 (mmt180) cc_final: 0.6256 (mmt180) REVERT: E 31 MET cc_start: 0.8397 (mmt) cc_final: 0.7980 (mmt) REVERT: E 89 GLU cc_start: 0.8816 (tp30) cc_final: 0.8549 (tm-30) REVERT: E 149 LYS cc_start: 0.8212 (tttt) cc_final: 0.8000 (tppt) REVERT: E 152 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8061 (tm-30) REVERT: E 323 GLN cc_start: 0.8548 (mt0) cc_final: 0.8210 (pt0) REVERT: E 405 MET cc_start: 0.8791 (mtp) cc_final: 0.8481 (mtp) REVERT: E 434 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7412 (tm-30) REVERT: E 515 MET cc_start: 0.7709 (tpp) cc_final: 0.7482 (tpp) REVERT: E 545 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8524 (m-30) REVERT: E 602 MET cc_start: 0.8544 (pmm) cc_final: 0.8337 (pmm) REVERT: E 609 GLN cc_start: 0.8600 (tp-100) cc_final: 0.8350 (tp40) REVERT: E 627 ARG cc_start: 0.6421 (OUTLIER) cc_final: 0.5905 (mmp80) REVERT: E 694 MET cc_start: 0.8320 (mtp) cc_final: 0.8008 (mtt) REVERT: F 310 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8061 (tp30) REVERT: F 416 ASN cc_start: 0.8025 (t0) cc_final: 0.7504 (t0) REVERT: F 461 TYR cc_start: 0.7944 (t80) cc_final: 0.7536 (t80) REVERT: F 515 MET cc_start: 0.8019 (mmt) cc_final: 0.7575 (mmt) REVERT: F 655 MET cc_start: 0.8379 (tpt) cc_final: 0.7947 (tpp) REVERT: F 674 ASP cc_start: 0.7472 (m-30) cc_final: 0.7081 (t0) REVERT: F 677 LYS cc_start: 0.7894 (mttt) cc_final: 0.7305 (tptt) REVERT: F 681 LYS cc_start: 0.8284 (mtpt) cc_final: 0.7939 (mtpp) REVERT: F 708 LEU cc_start: 0.8139 (tp) cc_final: 0.7828 (mp) REVERT: F 726 TYR cc_start: 0.8553 (t80) cc_final: 0.7531 (t80) outliers start: 85 outliers final: 53 residues processed: 608 average time/residue: 0.2226 time to fit residues: 224.3939 Evaluate side-chains 546 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 486 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 628 ARG Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 627 ARG Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain E residue 41 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 533 GLU Chi-restraints excluded: chain E residue 534 THR Chi-restraints excluded: chain E residue 545 ASP Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 627 ARG Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 624 ILE Chi-restraints excluded: chain F residue 672 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 204 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 198 optimal weight: 5.9990 chunk 224 optimal weight: 0.0870 chunk 168 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 286 optimal weight: 6.9990 chunk 241 optimal weight: 2.9990 chunk 199 optimal weight: 6.9990 chunk 242 optimal weight: 0.6980 overall best weight: 1.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.106822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.094564 restraints weight = 78401.077| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.84 r_work: 0.3326 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 37068 Z= 0.165 Angle : 0.614 12.772 50310 Z= 0.313 Chirality : 0.045 0.227 5526 Planarity : 0.004 0.040 6336 Dihedral : 7.368 162.008 5124 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.97 % Allowed : 15.00 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.13), residues: 4458 helix: 0.95 (0.11), residues: 2220 sheet: -0.85 (0.29), residues: 306 loop : -0.60 (0.15), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 12 TYR 0.043 0.001 TYR E 190 PHE 0.013 0.002 PHE B 94 TRP 0.056 0.001 TRP A 728 HIS 0.004 0.001 HIS C 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (37068) covalent geometry : angle 0.61445 / 0.31 (50310) hydrogen bonds : bond 0.03771 / 2.50 ( 1626) hydrogen bonds : angle 4.75824 / 3.35 ( 4644) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 504 time to evaluate : 1.752 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 21 ARG cc_start: 0.7471 (ttt180) cc_final: 0.6678 (mpt180) REVERT: A 26 CYS cc_start: 0.8054 (m) cc_final: 0.7798 (m) REVERT: A 55 GLU cc_start: 0.8912 (pt0) cc_final: 0.8662 (pt0) REVERT: A 89 GLU cc_start: 0.8841 (tp30) cc_final: 0.8436 (tm-30) REVERT: A 307 ASP cc_start: 0.8354 (t0) cc_final: 0.7792 (t0) REVERT: A 327 ASP cc_start: 0.8583 (t0) cc_final: 0.7918 (t0) REVERT: A 416 ASN cc_start: 0.8114 (t0) cc_final: 0.7522 (t0) REVERT: A 515 MET cc_start: 0.8066 (tpp) cc_final: 0.7342 (tpp) REVERT: A 677 LYS cc_start: 0.7904 (mttt) cc_final: 0.7274 (tptt) REVERT: A 681 LYS cc_start: 0.8392 (mtpt) cc_final: 0.7982 (mtpp) REVERT: A 708 LEU cc_start: 0.8271 (tp) cc_final: 0.7936 (mt) REVERT: B 21 ARG cc_start: 0.7751 (ttt180) cc_final: 0.6824 (mmt-90) REVERT: B 57 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8301 (m-30) REVERT: B 89 GLU cc_start: 0.8841 (tp30) cc_final: 0.8485 (tm-30) REVERT: B 253 SER cc_start: 0.9114 (m) cc_final: 0.8825 (t) REVERT: B 405 MET cc_start: 0.8835 (mtp) cc_final: 0.8528 (mtp) REVERT: B 431 GLU cc_start: 0.7617 (pm20) cc_final: 0.7310 (pm20) REVERT: B 433 VAL cc_start: 0.9132 (t) cc_final: 0.8874 (m) REVERT: B 438 LYS cc_start: 0.9220 (mttt) cc_final: 0.8869 (ttpp) REVERT: B 515 MET cc_start: 0.7617 (tpp) cc_final: 0.6861 (tpp) REVERT: B 545 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8479 (m-30) REVERT: B 609 GLN cc_start: 0.8687 (tp-100) cc_final: 0.8368 (tp40) REVERT: B 694 MET cc_start: 0.8197 (mtp) cc_final: 0.7897 (mtt) REVERT: B 708 LEU cc_start: 0.8418 (tp) cc_final: 0.8046 (mp) REVERT: C 14 MET cc_start: 0.8416 (mpp) cc_final: 0.7780 (mpp) REVERT: C 21 ARG cc_start: 0.7810 (ttt180) cc_final: 0.6779 (mpt180) REVERT: C 23 GLN cc_start: 0.8302 (tt0) cc_final: 0.7751 (pt0) REVERT: C 45 GLN cc_start: 0.8777 (tp40) cc_final: 0.8541 (tm-30) REVERT: C 57 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8142 (m-30) REVERT: C 313 ASP cc_start: 0.8297 (m-30) cc_final: 0.7871 (t0) REVERT: C 327 ASP cc_start: 0.8441 (m-30) cc_final: 0.8174 (t0) REVERT: C 416 ASN cc_start: 0.8106 (t0) cc_final: 0.7776 (t0) REVERT: C 431 GLU cc_start: 0.7596 (pm20) cc_final: 0.7291 (pm20) REVERT: C 444 CYS cc_start: 0.8114 (t) cc_final: 0.7832 (t) REVERT: C 453 MET cc_start: 0.8010 (tpp) cc_final: 0.7752 (tpp) REVERT: C 546 LEU cc_start: 0.9258 (mt) cc_final: 0.8973 (mt) REVERT: C 627 ARG cc_start: 0.6418 (OUTLIER) cc_final: 0.5582 (mmp80) REVERT: C 655 MET cc_start: 0.8550 (tpt) cc_final: 0.8252 (tpp) REVERT: C 694 MET cc_start: 0.8204 (mtp) cc_final: 0.7822 (mtt) REVERT: C 708 LEU cc_start: 0.8339 (tp) cc_final: 0.7753 (mp) REVERT: C 726 TYR cc_start: 0.8785 (t80) cc_final: 0.8359 (t80) REVERT: D 23 GLN cc_start: 0.8196 (tt0) cc_final: 0.7670 (pt0) REVERT: D 323 GLN cc_start: 0.8382 (mt0) cc_final: 0.8095 (pt0) REVERT: D 361 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8071 (tm-30) REVERT: D 388 GLN cc_start: 0.8707 (tp-100) cc_final: 0.8340 (tp-100) REVERT: D 416 ASN cc_start: 0.8048 (t0) cc_final: 0.7683 (t0) REVERT: D 429 CYS cc_start: 0.8822 (m) cc_final: 0.8530 (p) REVERT: D 438 LYS cc_start: 0.8957 (mptt) cc_final: 0.8731 (tmmt) REVERT: D 515 MET cc_start: 0.7789 (mmt) cc_final: 0.7526 (mmm) REVERT: D 627 ARG cc_start: 0.6615 (OUTLIER) cc_final: 0.5809 (mmp80) REVERT: D 655 MET cc_start: 0.8323 (tpt) cc_final: 0.8018 (tpp) REVERT: D 694 MET cc_start: 0.8088 (mtp) cc_final: 0.7743 (mtt) REVERT: D 708 LEU cc_start: 0.8287 (tp) cc_final: 0.7726 (mp) REVERT: D 723 MET cc_start: 0.5584 (mmt) cc_final: 0.5372 (mmt) REVERT: E 31 MET cc_start: 0.8414 (mmt) cc_final: 0.8053 (mmt) REVERT: E 89 GLU cc_start: 0.8814 (tp30) cc_final: 0.8444 (tm-30) REVERT: E 115 MET cc_start: 0.9026 (mmm) cc_final: 0.8724 (mtt) REVERT: E 149 LYS cc_start: 0.8058 (tttt) cc_final: 0.7852 (tppt) REVERT: E 152 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7982 (tm-30) REVERT: E 323 GLN cc_start: 0.8558 (mt0) cc_final: 0.8227 (pt0) REVERT: E 405 MET cc_start: 0.8805 (mtp) cc_final: 0.8490 (mtp) REVERT: E 545 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.8529 (m-30) REVERT: E 609 GLN cc_start: 0.8583 (tp-100) cc_final: 0.8335 (tp40) REVERT: E 627 ARG cc_start: 0.6438 (OUTLIER) cc_final: 0.5889 (mmp80) REVERT: E 657 ASN cc_start: 0.8948 (t0) cc_final: 0.8733 (t0) REVERT: E 694 MET cc_start: 0.8321 (mtp) cc_final: 0.8040 (mtt) REVERT: F 55 GLU cc_start: 0.8792 (pt0) cc_final: 0.8255 (pt0) REVERT: F 416 ASN cc_start: 0.8043 (t0) cc_final: 0.7525 (t0) REVERT: F 461 TYR cc_start: 0.7923 (t80) cc_final: 0.7527 (t80) REVERT: F 515 MET cc_start: 0.8048 (mmt) cc_final: 0.7604 (mmt) REVERT: F 546 LEU cc_start: 0.9236 (mt) cc_final: 0.8983 (mm) REVERT: F 655 MET cc_start: 0.8373 (tpt) cc_final: 0.8159 (tpp) REVERT: F 674 ASP cc_start: 0.7512 (m-30) cc_final: 0.7110 (t0) REVERT: F 677 LYS cc_start: 0.7872 (mttt) cc_final: 0.7208 (tptt) REVERT: F 681 LYS cc_start: 0.8296 (mtpt) cc_final: 0.7952 (mtpp) REVERT: F 708 LEU cc_start: 0.8162 (tp) cc_final: 0.7715 (mp) REVERT: F 726 TYR cc_start: 0.8566 (t80) cc_final: 0.7526 (t80) outliers start: 77 outliers final: 61 residues processed: 560 average time/residue: 0.2273 time to fit residues: 212.6441 Evaluate side-chains 552 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 484 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 628 ARG Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 627 ARG Chi-restraints excluded: chain D residue 628 ARG Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain E residue 41 MET Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 533 GLU Chi-restraints excluded: chain E residue 534 THR Chi-restraints excluded: chain E residue 545 ASP Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 627 ARG Chi-restraints excluded: chain E residue 669 ILE Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 624 ILE Chi-restraints excluded: chain F residue 627 ARG Chi-restraints excluded: chain F residue 672 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 45 optimal weight: 8.9990 chunk 382 optimal weight: 5.9990 chunk 353 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 201 optimal weight: 0.7980 chunk 277 optimal weight: 0.0170 chunk 281 optimal weight: 4.9990 chunk 225 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 chunk 266 optimal weight: 2.9990 overall best weight: 1.5222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 GLN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 724 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.108108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.095386 restraints weight = 79206.683| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.93 r_work: 0.3333 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 37068 Z= 0.153 Angle : 0.612 13.027 50310 Z= 0.311 Chirality : 0.045 0.217 5526 Planarity : 0.003 0.039 6336 Dihedral : 7.310 162.734 5124 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.00 % Allowed : 15.16 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.13), residues: 4458 helix: 0.97 (0.11), residues: 2220 sheet: -0.83 (0.30), residues: 306 loop : -0.56 (0.15), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 12 TYR 0.041 0.001 TYR E 190 PHE 0.013 0.002 PHE C 701 TRP 0.070 0.001 TRP A 728 HIS 0.011 0.001 HIS D 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (37068) covalent geometry : angle 0.61229 / 0.31 (50310) hydrogen bonds : bond 0.03665 / 2.43 ( 1626) hydrogen bonds : angle 4.72608 / 3.33 ( 4644) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 507 time to evaluate : 1.551 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 21 ARG cc_start: 0.7596 (ttt180) cc_final: 0.6684 (mpt180) REVERT: A 26 CYS cc_start: 0.8137 (m) cc_final: 0.7899 (m) REVERT: A 55 GLU cc_start: 0.8913 (pt0) cc_final: 0.8680 (pt0) REVERT: A 89 GLU cc_start: 0.8786 (tp30) cc_final: 0.8430 (tm-30) REVERT: A 307 ASP cc_start: 0.8371 (t0) cc_final: 0.7853 (t0) REVERT: A 327 ASP cc_start: 0.8623 (t0) cc_final: 0.7968 (t0) REVERT: A 416 ASN cc_start: 0.8105 (t0) cc_final: 0.7553 (t0) REVERT: A 515 MET cc_start: 0.8072 (tpp) cc_final: 0.7348 (tpp) REVERT: A 543 SER cc_start: 0.9280 (m) cc_final: 0.8621 (p) REVERT: A 677 LYS cc_start: 0.8078 (mttt) cc_final: 0.7424 (tptt) REVERT: A 681 LYS cc_start: 0.8376 (mtpt) cc_final: 0.7980 (mtpp) REVERT: A 708 LEU cc_start: 0.8221 (tp) cc_final: 0.7889 (mt) REVERT: B 21 ARG cc_start: 0.7762 (ttt180) cc_final: 0.6839 (mmt-90) REVERT: B 57 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.8278 (m-30) REVERT: B 89 GLU cc_start: 0.8832 (tp30) cc_final: 0.8477 (tm-30) REVERT: B 253 SER cc_start: 0.9096 (m) cc_final: 0.8807 (t) REVERT: B 323 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8114 (pm20) REVERT: B 405 MET cc_start: 0.8854 (mtp) cc_final: 0.8564 (mtp) REVERT: B 431 GLU cc_start: 0.7618 (pm20) cc_final: 0.7303 (pm20) REVERT: B 433 VAL cc_start: 0.9118 (t) cc_final: 0.8809 (m) REVERT: B 438 LYS cc_start: 0.9220 (mttt) cc_final: 0.8872 (ttpp) REVERT: B 515 MET cc_start: 0.7601 (tpp) cc_final: 0.6807 (tpp) REVERT: B 545 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8503 (m-30) REVERT: B 609 GLN cc_start: 0.8692 (tp-100) cc_final: 0.8386 (tp40) REVERT: B 694 MET cc_start: 0.8211 (mtp) cc_final: 0.7912 (mtt) REVERT: B 708 LEU cc_start: 0.8409 (tp) cc_final: 0.8028 (mp) REVERT: C 14 MET cc_start: 0.8403 (mpp) cc_final: 0.7762 (mpp) REVERT: C 21 ARG cc_start: 0.7830 (ttt180) cc_final: 0.6797 (mpt180) REVERT: C 23 GLN cc_start: 0.8230 (tt0) cc_final: 0.7713 (pt0) REVERT: C 45 GLN cc_start: 0.8844 (tp40) cc_final: 0.8564 (tm-30) REVERT: C 57 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8110 (m-30) REVERT: C 313 ASP cc_start: 0.8282 (m-30) cc_final: 0.7869 (t0) REVERT: C 327 ASP cc_start: 0.8439 (m-30) cc_final: 0.8176 (t0) REVERT: C 405 MET cc_start: 0.8997 (mtm) cc_final: 0.8699 (mtt) REVERT: C 416 ASN cc_start: 0.8147 (t0) cc_final: 0.7820 (t0) REVERT: C 431 GLU cc_start: 0.7615 (pm20) cc_final: 0.7315 (pm20) REVERT: C 444 CYS cc_start: 0.8107 (t) cc_final: 0.7863 (t) REVERT: C 453 MET cc_start: 0.7987 (tpp) cc_final: 0.7742 (tpp) REVERT: C 546 LEU cc_start: 0.9254 (mt) cc_final: 0.8973 (mt) REVERT: C 627 ARG cc_start: 0.6452 (OUTLIER) cc_final: 0.5610 (mmp80) REVERT: C 655 MET cc_start: 0.8388 (tpt) cc_final: 0.7963 (tpp) REVERT: C 694 MET cc_start: 0.8176 (mtp) cc_final: 0.7603 (mtt) REVERT: C 708 LEU cc_start: 0.8346 (tp) cc_final: 0.7740 (mp) REVERT: D 23 GLN cc_start: 0.8318 (tt0) cc_final: 0.7759 (pt0) REVERT: D 323 GLN cc_start: 0.8367 (mt0) cc_final: 0.8093 (pt0) REVERT: D 339 MET cc_start: 0.8108 (ttp) cc_final: 0.7590 (ptm) REVERT: D 361 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8093 (tm-30) REVERT: D 388 GLN cc_start: 0.8689 (tp-100) cc_final: 0.8331 (tp-100) REVERT: D 429 CYS cc_start: 0.8797 (m) cc_final: 0.8529 (p) REVERT: D 438 LYS cc_start: 0.8949 (mptt) cc_final: 0.8739 (tmmt) REVERT: D 515 MET cc_start: 0.7737 (mmt) cc_final: 0.7466 (mmm) REVERT: D 627 ARG cc_start: 0.6617 (OUTLIER) cc_final: 0.5828 (mmp80) REVERT: D 655 MET cc_start: 0.8290 (tpt) cc_final: 0.7925 (tpp) REVERT: D 694 MET cc_start: 0.8184 (mtp) cc_final: 0.7869 (mtt) REVERT: D 708 LEU cc_start: 0.8260 (tp) cc_final: 0.7687 (mp) REVERT: D 723 MET cc_start: 0.5340 (mmt) cc_final: 0.5065 (mmt) REVERT: E 12 ARG cc_start: 0.6846 (mmt180) cc_final: 0.6571 (mmt180) REVERT: E 31 MET cc_start: 0.8395 (mmt) cc_final: 0.8072 (mmt) REVERT: E 89 GLU cc_start: 0.8789 (tp30) cc_final: 0.8525 (tm-30) REVERT: E 115 MET cc_start: 0.9047 (mmm) cc_final: 0.8749 (mtt) REVERT: E 152 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8023 (tm-30) REVERT: E 172 MET cc_start: 0.8438 (mmm) cc_final: 0.7967 (mmm) REVERT: E 323 GLN cc_start: 0.8562 (mt0) cc_final: 0.8234 (pt0) REVERT: E 405 MET cc_start: 0.8801 (mtp) cc_final: 0.8502 (mtp) REVERT: E 423 ILE cc_start: 0.9534 (mp) cc_final: 0.9244 (mm) REVERT: E 545 ASP cc_start: 0.8813 (OUTLIER) cc_final: 0.8529 (m-30) REVERT: E 602 MET cc_start: 0.8431 (pmm) cc_final: 0.8062 (pmm) REVERT: E 627 ARG cc_start: 0.6427 (OUTLIER) cc_final: 0.5877 (mmp80) REVERT: E 694 MET cc_start: 0.8276 (mtp) cc_final: 0.7978 (mtt) REVERT: F 14 MET cc_start: 0.8029 (mpp) cc_final: 0.7210 (mpp) REVERT: F 55 GLU cc_start: 0.8781 (pt0) cc_final: 0.8234 (pt0) REVERT: F 416 ASN cc_start: 0.8039 (t0) cc_final: 0.7531 (t0) REVERT: F 461 TYR cc_start: 0.7886 (t80) cc_final: 0.7555 (t80) REVERT: F 515 MET cc_start: 0.8033 (mmt) cc_final: 0.7595 (mmt) REVERT: F 546 LEU cc_start: 0.9248 (mt) cc_final: 0.8992 (mm) REVERT: F 655 MET cc_start: 0.8349 (tpt) cc_final: 0.8142 (tpp) REVERT: F 674 ASP cc_start: 0.7526 (m-30) cc_final: 0.7168 (t0) REVERT: F 677 LYS cc_start: 0.7908 (mttt) cc_final: 0.7305 (tptt) REVERT: F 681 LYS cc_start: 0.8294 (mtpt) cc_final: 0.7957 (mtpp) REVERT: F 708 LEU cc_start: 0.8167 (tp) cc_final: 0.7848 (mp) REVERT: F 726 TYR cc_start: 0.8622 (t80) cc_final: 0.7579 (t80) outliers start: 78 outliers final: 63 residues processed: 563 average time/residue: 0.2222 time to fit residues: 209.1776 Evaluate side-chains 550 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 479 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 628 ARG Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 627 ARG Chi-restraints excluded: chain D residue 628 ARG Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 534 THR Chi-restraints excluded: chain E residue 545 ASP Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 627 ARG Chi-restraints excluded: chain E residue 669 ILE Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 624 ILE Chi-restraints excluded: chain F residue 627 ARG Chi-restraints excluded: chain F residue 672 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 248 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 252 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 267 optimal weight: 0.0070 chunk 436 optimal weight: 5.9990 chunk 270 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 overall best weight: 2.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 418 GLN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 GLN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.106007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.093711 restraints weight = 78046.357| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.87 r_work: 0.3308 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 37068 Z= 0.195 Angle : 0.653 16.066 50310 Z= 0.332 Chirality : 0.046 0.232 5526 Planarity : 0.004 0.040 6336 Dihedral : 7.478 166.599 5124 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.07 % Allowed : 15.16 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.13), residues: 4458 helix: 0.93 (0.11), residues: 2208 sheet: -0.79 (0.30), residues: 306 loop : -0.56 (0.15), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 12 TYR 0.042 0.002 TYR E 190 PHE 0.016 0.002 PHE C 701 TRP 0.084 0.002 TRP F 728 HIS 0.006 0.001 HIS C 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 (37068) covalent geometry : angle 0.65284 / 0.33 (50310) hydrogen bonds : bond 0.03964 / 2.63 ( 1626) hydrogen bonds : angle 4.86228 / 3.42 ( 4644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7740.45 seconds wall clock time: 134 minutes 25.55 seconds (8065.55 seconds total)