Starting phenix.real_space_refine on Fri Mar 6 14:01:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uaj_20707/03_2026/6uaj_20707.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uaj_20707/03_2026/6uaj_20707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6uaj_20707/03_2026/6uaj_20707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uaj_20707/03_2026/6uaj_20707.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uaj_20707/03_2026/6uaj_20707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uaj_20707/03_2026/6uaj_20707.map" } resolution = 3.84 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= 0.128 sd= 3.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 96 5.49 5 S 168 5.16 5 C 19240 2.51 5 N 5336 2.21 5 O 6192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31032 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3717 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 471} Chain breaks: 1 Chain: "B" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3717 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 471} Chain breaks: 1 Chain: "C" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3717 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 471} Chain breaks: 1 Chain: "D" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3717 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 471} Chain breaks: 1 Chain: "E" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3717 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 471} Chain breaks: 1 Chain: "F" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3717 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 471} Chain breaks: 1 Chain: "G" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3717 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 471} Chain breaks: 1 Chain: "H" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3717 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 471} Chain breaks: 1 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Time building chain proxies: 6.47, per 1000 atoms: 0.21 Number of scatterers: 31032 At special positions: 0 Unit cell: (150.15, 150.15, 116.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 168 16.00 P 96 15.00 O 6192 8.00 N 5336 7.00 C 19240 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 1.3 seconds 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7104 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 48 sheets defined 34.4% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.963A pdb=" N GLN A 48 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 85 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 126 through 136 removed outlier: 4.014A pdb=" N VAL A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 203 removed outlier: 3.875A pdb=" N ALA A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 233 removed outlier: 3.516A pdb=" N LYS A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 280 through 292 removed outlier: 3.644A pdb=" N ILE A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 removed outlier: 3.917A pdb=" N ASP A 315 " --> pdb=" O LYS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 355 removed outlier: 3.506A pdb=" N ALA A 346 " --> pdb=" O PRO A 342 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 370 through 380 removed outlier: 3.814A pdb=" N ALA A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 420 removed outlier: 3.798A pdb=" N ALA A 419 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET A 420 " --> pdb=" O LEU A 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 420' Processing helix chain 'A' and resid 452 through 470 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 496 through 502 Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.964A pdb=" N GLN B 48 " --> pdb=" O THR B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 126 through 136 removed outlier: 4.013A pdb=" N VAL B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 203 removed outlier: 3.874A pdb=" N ALA B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 233 removed outlier: 3.515A pdb=" N LYS B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 255 No H-bonds generated for 'chain 'B' and resid 253 through 255' Processing helix chain 'B' and resid 256 through 266 Processing helix chain 'B' and resid 280 through 292 removed outlier: 3.643A pdb=" N ILE B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 removed outlier: 3.917A pdb=" N ASP B 315 " --> pdb=" O LYS B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.506A pdb=" N ALA B 346 " --> pdb=" O PRO B 342 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 370 through 380 removed outlier: 3.813A pdb=" N ALA B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 420 removed outlier: 3.798A pdb=" N ALA B 419 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET B 420 " --> pdb=" O LEU B 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 420' Processing helix chain 'B' and resid 452 through 470 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 496 through 502 Processing helix chain 'C' and resid 45 through 49 removed outlier: 3.963A pdb=" N GLN C 48 " --> pdb=" O THR C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 126 through 136 removed outlier: 4.014A pdb=" N VAL C 130 " --> pdb=" O ARG C 126 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE C 131 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 203 removed outlier: 3.874A pdb=" N ALA C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 233 removed outlier: 3.514A pdb=" N LYS C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 256 through 266 Processing helix chain 'C' and resid 280 through 292 removed outlier: 3.643A pdb=" N ILE C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 removed outlier: 3.917A pdb=" N ASP C 315 " --> pdb=" O LYS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 355 removed outlier: 3.506A pdb=" N ALA C 346 " --> pdb=" O PRO C 342 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 358 No H-bonds generated for 'chain 'C' and resid 356 through 358' Processing helix chain 'C' and resid 370 through 380 removed outlier: 3.813A pdb=" N ALA C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 420 removed outlier: 3.798A pdb=" N ALA C 419 " --> pdb=" O SER C 416 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET C 420 " --> pdb=" O LEU C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 420' Processing helix chain 'C' and resid 452 through 470 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 496 through 502 Processing helix chain 'D' and resid 45 through 49 removed outlier: 3.963A pdb=" N GLN D 48 " --> pdb=" O THR D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 85 Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 126 through 136 removed outlier: 4.013A pdb=" N VAL D 130 " --> pdb=" O ARG D 126 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE D 131 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU D 132 " --> pdb=" O ARG D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 203 removed outlier: 3.874A pdb=" N ALA D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 233 removed outlier: 3.515A pdb=" N LYS D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 256 through 266 Processing helix chain 'D' and resid 280 through 292 removed outlier: 3.643A pdb=" N ILE D 284 " --> pdb=" O SER D 280 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 315 removed outlier: 3.917A pdb=" N ASP D 315 " --> pdb=" O LYS D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 355 removed outlier: 3.506A pdb=" N ALA D 346 " --> pdb=" O PRO D 342 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 358 No H-bonds generated for 'chain 'D' and resid 356 through 358' Processing helix chain 'D' and resid 370 through 380 removed outlier: 3.814A pdb=" N ALA D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 420 removed outlier: 3.799A pdb=" N ALA D 419 " --> pdb=" O SER D 416 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET D 420 " --> pdb=" O LEU D 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 420' Processing helix chain 'D' and resid 452 through 470 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 496 through 502 Processing helix chain 'E' and resid 45 through 49 removed outlier: 3.963A pdb=" N GLN E 48 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 85 Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 126 through 136 removed outlier: 4.014A pdb=" N VAL E 130 " --> pdb=" O ARG E 126 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE E 131 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 203 removed outlier: 3.875A pdb=" N ALA E 197 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 233 removed outlier: 3.515A pdb=" N LYS E 228 " --> pdb=" O ARG E 224 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR E 233 " --> pdb=" O LYS E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 255 No H-bonds generated for 'chain 'E' and resid 253 through 255' Processing helix chain 'E' and resid 256 through 266 Processing helix chain 'E' and resid 280 through 292 removed outlier: 3.643A pdb=" N ILE E 284 " --> pdb=" O SER E 280 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 315 removed outlier: 3.917A pdb=" N ASP E 315 " --> pdb=" O LYS E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 355 removed outlier: 3.506A pdb=" N ALA E 346 " --> pdb=" O PRO E 342 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 358 No H-bonds generated for 'chain 'E' and resid 356 through 358' Processing helix chain 'E' and resid 370 through 380 removed outlier: 3.813A pdb=" N ALA E 374 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 420 removed outlier: 3.799A pdb=" N ALA E 419 " --> pdb=" O SER E 416 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET E 420 " --> pdb=" O LEU E 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 416 through 420' Processing helix chain 'E' and resid 452 through 470 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 496 through 502 Processing helix chain 'F' and resid 45 through 49 removed outlier: 3.964A pdb=" N GLN F 48 " --> pdb=" O THR F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 85 Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 126 through 136 removed outlier: 4.014A pdb=" N VAL F 130 " --> pdb=" O ARG F 126 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE F 131 " --> pdb=" O VAL F 127 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU F 132 " --> pdb=" O ARG F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 203 removed outlier: 3.874A pdb=" N ALA F 197 " --> pdb=" O THR F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 233 removed outlier: 3.516A pdb=" N LYS F 228 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR F 233 " --> pdb=" O LYS F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 255 No H-bonds generated for 'chain 'F' and resid 253 through 255' Processing helix chain 'F' and resid 256 through 266 Processing helix chain 'F' and resid 280 through 292 removed outlier: 3.643A pdb=" N ILE F 284 " --> pdb=" O SER F 280 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 315 removed outlier: 3.916A pdb=" N ASP F 315 " --> pdb=" O LYS F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 355 removed outlier: 3.506A pdb=" N ALA F 346 " --> pdb=" O PRO F 342 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 358 No H-bonds generated for 'chain 'F' and resid 356 through 358' Processing helix chain 'F' and resid 370 through 380 removed outlier: 3.813A pdb=" N ALA F 374 " --> pdb=" O VAL F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 420 removed outlier: 3.798A pdb=" N ALA F 419 " --> pdb=" O SER F 416 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET F 420 " --> pdb=" O LEU F 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 416 through 420' Processing helix chain 'F' and resid 452 through 470 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 496 through 502 Processing helix chain 'G' and resid 45 through 49 removed outlier: 3.964A pdb=" N GLN G 48 " --> pdb=" O THR G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 85 Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'G' and resid 126 through 136 removed outlier: 4.014A pdb=" N VAL G 130 " --> pdb=" O ARG G 126 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE G 131 " --> pdb=" O VAL G 127 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU G 132 " --> pdb=" O ARG G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 203 removed outlier: 3.875A pdb=" N ALA G 197 " --> pdb=" O THR G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 233 removed outlier: 3.515A pdb=" N LYS G 228 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR G 233 " --> pdb=" O LYS G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 255 No H-bonds generated for 'chain 'G' and resid 253 through 255' Processing helix chain 'G' and resid 256 through 266 Processing helix chain 'G' and resid 280 through 292 removed outlier: 3.643A pdb=" N ILE G 284 " --> pdb=" O SER G 280 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 315 removed outlier: 3.916A pdb=" N ASP G 315 " --> pdb=" O LYS G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 355 removed outlier: 3.506A pdb=" N ALA G 346 " --> pdb=" O PRO G 342 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 356 through 358 No H-bonds generated for 'chain 'G' and resid 356 through 358' Processing helix chain 'G' and resid 370 through 380 removed outlier: 3.813A pdb=" N ALA G 374 " --> pdb=" O VAL G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 420 removed outlier: 3.799A pdb=" N ALA G 419 " --> pdb=" O SER G 416 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET G 420 " --> pdb=" O LEU G 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 416 through 420' Processing helix chain 'G' and resid 452 through 470 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'G' and resid 496 through 502 Processing helix chain 'H' and resid 45 through 49 removed outlier: 3.963A pdb=" N GLN H 48 " --> pdb=" O THR H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 85 Processing helix chain 'H' and resid 96 through 109 Processing helix chain 'H' and resid 126 through 136 removed outlier: 4.013A pdb=" N VAL H 130 " --> pdb=" O ARG H 126 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE H 131 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU H 132 " --> pdb=" O ARG H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 203 removed outlier: 3.874A pdb=" N ALA H 197 " --> pdb=" O THR H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 233 removed outlier: 3.515A pdb=" N LYS H 228 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR H 233 " --> pdb=" O LYS H 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 255 No H-bonds generated for 'chain 'H' and resid 253 through 255' Processing helix chain 'H' and resid 256 through 266 Processing helix chain 'H' and resid 280 through 292 removed outlier: 3.643A pdb=" N ILE H 284 " --> pdb=" O SER H 280 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 315 removed outlier: 3.917A pdb=" N ASP H 315 " --> pdb=" O LYS H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 355 removed outlier: 3.506A pdb=" N ALA H 346 " --> pdb=" O PRO H 342 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 356 through 358 No H-bonds generated for 'chain 'H' and resid 356 through 358' Processing helix chain 'H' and resid 370 through 380 removed outlier: 3.813A pdb=" N ALA H 374 " --> pdb=" O VAL H 370 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 420 removed outlier: 3.798A pdb=" N ALA H 419 " --> pdb=" O SER H 416 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET H 420 " --> pdb=" O LEU H 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 416 through 420' Processing helix chain 'H' and resid 452 through 470 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 496 through 502 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 66 removed outlier: 6.477A pdb=" N VAL A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N MET A 385 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N ARG A 322 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY A 301 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL A 271 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLY A 302 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU A 273 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N VAL A 304 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 145 removed outlier: 3.734A pdb=" N ILE A 142 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 189 removed outlier: 6.041A pdb=" N ALA A 188 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 403 Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 65 through 66 removed outlier: 6.477A pdb=" N VAL B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N MET B 385 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N ARG B 322 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY B 301 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL B 271 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLY B 302 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU B 273 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N VAL B 304 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA B 248 " --> pdb=" O VAL B 272 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 142 through 145 removed outlier: 3.734A pdb=" N ILE B 142 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 188 through 189 removed outlier: 6.040A pdb=" N ALA B 188 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 401 through 403 Processing sheet with id=AB4, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 65 through 66 removed outlier: 6.478A pdb=" N VAL C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N MET C 385 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N ARG C 322 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY C 301 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL C 271 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLY C 302 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N LEU C 273 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N VAL C 304 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 142 through 145 removed outlier: 3.734A pdb=" N ILE C 142 " --> pdb=" O ILE C 158 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 188 through 189 removed outlier: 6.041A pdb=" N ALA C 188 " --> pdb=" O VAL C 212 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 401 through 403 Processing sheet with id=AC1, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 65 through 66 removed outlier: 6.478A pdb=" N VAL D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N MET D 385 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N ARG D 322 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLY D 301 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL D 271 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLY D 302 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU D 273 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N VAL D 304 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA D 248 " --> pdb=" O VAL D 272 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 142 through 145 removed outlier: 3.734A pdb=" N ILE D 142 " --> pdb=" O ILE D 158 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 188 through 189 removed outlier: 6.040A pdb=" N ALA D 188 " --> pdb=" O VAL D 212 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 401 through 403 Processing sheet with id=AC7, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 65 through 66 removed outlier: 6.478A pdb=" N VAL E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N MET E 385 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N ARG E 322 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY E 301 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL E 271 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLY E 302 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU E 273 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N VAL E 304 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 142 through 145 removed outlier: 3.734A pdb=" N ILE E 142 " --> pdb=" O ILE E 158 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 188 through 189 removed outlier: 6.041A pdb=" N ALA E 188 " --> pdb=" O VAL E 212 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 401 through 403 Processing sheet with id=AD4, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AD5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'F' and resid 65 through 66 removed outlier: 6.477A pdb=" N VAL F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N MET F 385 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N ARG F 322 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY F 301 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL F 271 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLY F 302 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU F 273 " --> pdb=" O GLY F 302 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N VAL F 304 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA F 248 " --> pdb=" O VAL F 272 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 142 through 145 removed outlier: 3.734A pdb=" N ILE F 142 " --> pdb=" O ILE F 158 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 188 through 189 removed outlier: 6.041A pdb=" N ALA F 188 " --> pdb=" O VAL F 212 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 401 through 403 Processing sheet with id=AE1, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AE2, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE3, first strand: chain 'G' and resid 65 through 66 removed outlier: 6.478A pdb=" N VAL G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N MET G 385 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N ARG G 322 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY G 301 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL G 271 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLY G 302 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU G 273 " --> pdb=" O GLY G 302 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N VAL G 304 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA G 248 " --> pdb=" O VAL G 272 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 142 through 145 removed outlier: 3.733A pdb=" N ILE G 142 " --> pdb=" O ILE G 158 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 188 through 189 removed outlier: 6.041A pdb=" N ALA G 188 " --> pdb=" O VAL G 212 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 401 through 403 Processing sheet with id=AE7, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AE8, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AE9, first strand: chain 'H' and resid 65 through 66 removed outlier: 6.478A pdb=" N VAL H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N MET H 385 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N ARG H 322 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLY H 301 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL H 271 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLY H 302 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU H 273 " --> pdb=" O GLY H 302 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N VAL H 304 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 142 through 145 removed outlier: 3.735A pdb=" N ILE H 142 " --> pdb=" O ILE H 158 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 188 through 189 removed outlier: 6.041A pdb=" N ALA H 188 " --> pdb=" O VAL H 212 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 401 through 403 832 hydrogen bonds defined for protein. 2376 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: 5.94 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 5210 1.30 - 1.43: 7481 1.43 - 1.55: 18337 1.55 - 1.68: 268 1.68 - 1.80: 280 Bond restraints: 31576 Sorted by residual: bond pdb=" C2' ATP F 603 " pdb=" C3' ATP F 603 " ideal model delta sigma weight residual 1.531 1.252 0.279 1.20e-02 6.94e+03 5.40e+02 bond pdb=" C2' ATP A 603 " pdb=" C3' ATP A 603 " ideal model delta sigma weight residual 1.531 1.252 0.279 1.20e-02 6.94e+03 5.39e+02 bond pdb=" C2' ATP B 603 " pdb=" C3' ATP B 603 " ideal model delta sigma weight residual 1.531 1.253 0.278 1.20e-02 6.94e+03 5.37e+02 bond pdb=" C2' ATP D 603 " pdb=" C3' ATP D 603 " ideal model delta sigma weight residual 1.531 1.253 0.278 1.20e-02 6.94e+03 5.36e+02 bond pdb=" C2' ATP C 603 " pdb=" C3' ATP C 603 " ideal model delta sigma weight residual 1.531 1.253 0.278 1.20e-02 6.94e+03 5.36e+02 ... (remaining 31571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.11: 41487 4.11 - 8.22: 1061 8.22 - 12.34: 180 12.34 - 16.45: 80 16.45 - 20.56: 80 Bond angle restraints: 42888 Sorted by residual: angle pdb=" PB ATP D 603 " pdb=" O3B ATP D 603 " pdb=" PG ATP D 603 " ideal model delta sigma weight residual 139.87 121.11 18.76 1.00e+00 1.00e+00 3.52e+02 angle pdb=" PB ATP A 603 " pdb=" O3B ATP A 603 " pdb=" PG ATP A 603 " ideal model delta sigma weight residual 139.87 121.13 18.74 1.00e+00 1.00e+00 3.51e+02 angle pdb=" PB ATP E 603 " pdb=" O3B ATP E 603 " pdb=" PG ATP E 603 " ideal model delta sigma weight residual 139.87 121.14 18.73 1.00e+00 1.00e+00 3.51e+02 angle pdb=" PB ATP H 603 " pdb=" O3B ATP H 603 " pdb=" PG ATP H 603 " ideal model delta sigma weight residual 139.87 121.15 18.72 1.00e+00 1.00e+00 3.50e+02 angle pdb=" PB ATP F 603 " pdb=" O3B ATP F 603 " pdb=" PG ATP F 603 " ideal model delta sigma weight residual 139.87 121.16 18.71 1.00e+00 1.00e+00 3.50e+02 ... (remaining 42883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.54: 18284 34.54 - 69.09: 920 69.09 - 103.63: 124 103.63 - 138.18: 8 138.18 - 172.72: 32 Dihedral angle restraints: 19368 sinusoidal: 8248 harmonic: 11120 Sorted by residual: dihedral pdb=" C1' IMP C 604 " pdb=" C2' IMP C 604 " pdb=" C3' IMP C 604 " pdb=" C4' IMP C 604 " ideal model delta sinusoidal sigma weight residual -35.00 17.35 -52.35 1 8.00e+00 1.56e-02 5.84e+01 dihedral pdb=" C1' IMP D 604 " pdb=" C2' IMP D 604 " pdb=" C3' IMP D 604 " pdb=" C4' IMP D 604 " ideal model delta sinusoidal sigma weight residual -35.00 17.30 -52.30 1 8.00e+00 1.56e-02 5.83e+01 dihedral pdb=" C1' IMP H 604 " pdb=" C2' IMP H 604 " pdb=" C3' IMP H 604 " pdb=" C4' IMP H 604 " ideal model delta sinusoidal sigma weight residual -35.00 17.28 -52.28 1 8.00e+00 1.56e-02 5.82e+01 ... (remaining 19365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 4436 0.130 - 0.260: 388 0.260 - 0.390: 48 0.390 - 0.520: 8 0.520 - 0.650: 8 Chirality restraints: 4888 Sorted by residual: chirality pdb=" CB ILE C 115 " pdb=" CA ILE C 115 " pdb=" CG1 ILE C 115 " pdb=" CG2 ILE C 115 " both_signs ideal model delta sigma weight residual False 2.64 1.99 0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CB ILE E 115 " pdb=" CA ILE E 115 " pdb=" CG1 ILE E 115 " pdb=" CG2 ILE E 115 " both_signs ideal model delta sigma weight residual False 2.64 2.00 0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CB ILE D 115 " pdb=" CA ILE D 115 " pdb=" CG1 ILE D 115 " pdb=" CG2 ILE D 115 " both_signs ideal model delta sigma weight residual False 2.64 2.00 0.65 2.00e-01 2.50e+01 1.05e+01 ... (remaining 4885 not shown) Planarity restraints: 5328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE G 115 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.26e+01 pdb=" C ILE G 115 " 0.061 2.00e-02 2.50e+03 pdb=" O ILE G 115 " -0.024 2.00e-02 2.50e+03 pdb=" N THR G 116 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 115 " 0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C ILE A 115 " -0.061 2.00e-02 2.50e+03 pdb=" O ILE A 115 " 0.023 2.00e-02 2.50e+03 pdb=" N THR A 116 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 115 " -0.017 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C ILE F 115 " 0.061 2.00e-02 2.50e+03 pdb=" O ILE F 115 " -0.023 2.00e-02 2.50e+03 pdb=" N THR F 116 " -0.020 2.00e-02 2.50e+03 ... (remaining 5325 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 9296 2.80 - 3.33: 31206 3.33 - 3.85: 55539 3.85 - 4.38: 63598 4.38 - 4.90: 102488 Nonbonded interactions: 262127 Sorted by model distance: nonbonded pdb=" N GLU E 487 " pdb=" OE1 GLU E 487 " model vdw 2.275 3.120 nonbonded pdb=" N GLU G 487 " pdb=" OE1 GLU G 487 " model vdw 2.275 3.120 nonbonded pdb=" N GLU A 487 " pdb=" OE1 GLU A 487 " model vdw 2.275 3.120 nonbonded pdb=" N GLU F 487 " pdb=" OE1 GLU F 487 " model vdw 2.275 3.120 nonbonded pdb=" N GLU C 487 " pdb=" OE1 GLU C 487 " model vdw 2.276 3.120 ... (remaining 262122 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' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 25.410 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 : 0.018 0.288 31592 Z= 0.998 Angle : 1.861 20.561 42888 Z= 1.024 Chirality : 0.086 0.650 4888 Planarity : 0.008 0.068 5328 Dihedral : 20.747 172.723 12264 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 12.03 % Allowed : 14.54 % Favored : 73.43 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -4.34 (0.11), residues: 3880 helix: -3.42 (0.10), residues: 1200 sheet: -3.60 (0.18), residues: 376 loop : -2.49 (0.11), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG C 224 TYR 0.015 0.003 TYR C 233 PHE 0.024 0.004 PHE H 456 HIS 0.016 0.003 HIS E 171 Details of bonding type rmsd covalent geometry : bond 0.01809 (31576) covalent geometry : angle 1.86090 (42888) hydrogen bonds : bond 0.19900 ( 832) hydrogen bonds : angle 7.99348 ( 2376) Misc. bond : bond 0.00044 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1779 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 384 poor density : 1395 time to evaluate : 1.025 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: 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 18 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8690 (tm) REVERT: A 19 THR cc_start: 0.8678 (p) cc_final: 0.8252 (t) REVERT: A 32 TYR cc_start: 0.8723 (m-80) cc_final: 0.8420 (m-10) REVERT: A 95 CYS cc_start: 0.8545 (p) cc_final: 0.8320 (p) REVERT: A 128 ARG cc_start: 0.8980 (mmt90) cc_final: 0.8595 (mmt90) REVERT: A 144 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.9039 (pp) REVERT: A 202 GLN cc_start: 0.9418 (mt0) cc_final: 0.8362 (mt0) REVERT: A 205 LYS cc_start: 0.9366 (mppt) cc_final: 0.9128 (mttt) REVERT: A 208 LYS cc_start: 0.8512 (mtpp) cc_final: 0.8051 (mtpt) REVERT: A 214 GLU cc_start: 0.9436 (mm-30) cc_final: 0.9212 (mp0) REVERT: A 250 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.7922 (pp) REVERT: A 284 ILE cc_start: 0.9492 (OUTLIER) cc_final: 0.9207 (mp) REVERT: A 285 ASN cc_start: 0.9435 (m110) cc_final: 0.9071 (m-40) REVERT: A 311 LYS cc_start: 0.8935 (tmtt) cc_final: 0.8365 (tptt) REVERT: A 351 SER cc_start: 0.8952 (OUTLIER) cc_final: 0.8672 (t) REVERT: A 379 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9157 (tm) REVERT: A 386 MET cc_start: 0.8983 (ppp) cc_final: 0.8249 (ppp) REVERT: A 407 ARG cc_start: 0.7336 (ttt180) cc_final: 0.6636 (ttt180) REVERT: A 482 MET cc_start: 0.8448 (tpt) cc_final: 0.8155 (tpt) REVERT: A 489 LYS cc_start: 0.8479 (ttmm) cc_final: 0.8212 (tptm) REVERT: A 490 PHE cc_start: 0.8119 (m-80) cc_final: 0.7872 (m-80) REVERT: A 509 TYR cc_start: 0.7708 (p90) cc_final: 0.7117 (p90) REVERT: A 514 PHE cc_start: 0.7356 (p90) cc_final: 0.6849 (p90) REVERT: B 128 ARG cc_start: 0.8987 (mmt90) cc_final: 0.8760 (mmm-85) REVERT: B 194 LEU cc_start: 0.9502 (tp) cc_final: 0.9145 (tp) REVERT: B 199 GLU cc_start: 0.9384 (tp30) cc_final: 0.8949 (tp30) REVERT: B 202 GLN cc_start: 0.9419 (mt0) cc_final: 0.8355 (mt0) REVERT: B 203 ARG cc_start: 0.9125 (ptp-110) cc_final: 0.8905 (ptp-110) REVERT: B 205 LYS cc_start: 0.9363 (mppt) cc_final: 0.9141 (mttt) REVERT: B 208 LYS cc_start: 0.8354 (mtpp) cc_final: 0.8113 (ttmm) REVERT: B 214 GLU cc_start: 0.9387 (mm-30) cc_final: 0.9167 (mp0) REVERT: B 216 ASP cc_start: 0.9021 (t70) cc_final: 0.8745 (t0) REVERT: B 284 ILE cc_start: 0.9452 (OUTLIER) cc_final: 0.9220 (mp) REVERT: B 285 ASN cc_start: 0.9309 (m110) cc_final: 0.8932 (m110) REVERT: B 311 LYS cc_start: 0.9102 (tmtt) cc_final: 0.8542 (tptt) REVERT: B 353 TYR cc_start: 0.8303 (t80) cc_final: 0.8066 (t80) REVERT: B 357 PHE cc_start: 0.8807 (m-80) cc_final: 0.8242 (m-10) REVERT: B 386 MET cc_start: 0.8901 (ppp) cc_final: 0.8285 (ppp) REVERT: B 401 PHE cc_start: 0.8317 (p90) cc_final: 0.8096 (p90) REVERT: B 407 ARG cc_start: 0.7387 (ttt180) cc_final: 0.6748 (ttt180) REVERT: B 420 MET cc_start: 0.6106 (tpp) cc_final: 0.5868 (mmm) REVERT: B 470 ASP cc_start: 0.8732 (m-30) cc_final: 0.8523 (m-30) REVERT: B 482 MET cc_start: 0.8497 (tpt) cc_final: 0.8180 (tpt) REVERT: B 490 PHE cc_start: 0.8142 (m-80) cc_final: 0.7790 (m-80) REVERT: B 509 TYR cc_start: 0.7760 (p90) cc_final: 0.7110 (p90) REVERT: B 514 PHE cc_start: 0.7283 (p90) cc_final: 0.6920 (p90) REVERT: C 18 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8723 (tm) REVERT: C 19 THR cc_start: 0.8618 (p) cc_final: 0.8245 (t) REVERT: C 32 TYR cc_start: 0.8743 (m-80) cc_final: 0.8490 (m-10) REVERT: C 128 ARG cc_start: 0.9000 (mmt90) cc_final: 0.8777 (mmm-85) REVERT: C 144 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.9070 (pp) REVERT: C 199 GLU cc_start: 0.9392 (tp30) cc_final: 0.8859 (tp30) REVERT: C 202 GLN cc_start: 0.9461 (mt0) cc_final: 0.8530 (mt0) REVERT: C 203 ARG cc_start: 0.9084 (ptp-110) cc_final: 0.8840 (ptp-110) REVERT: C 205 LYS cc_start: 0.9361 (mppt) cc_final: 0.9127 (mttt) REVERT: C 208 LYS cc_start: 0.8468 (mtpp) cc_final: 0.8004 (mtpt) REVERT: C 214 GLU cc_start: 0.9417 (mm-30) cc_final: 0.9179 (mp0) REVERT: C 216 ASP cc_start: 0.9109 (t70) cc_final: 0.8838 (t0) REVERT: C 250 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7624 (pp) REVERT: C 284 ILE cc_start: 0.9488 (OUTLIER) cc_final: 0.9231 (mp) REVERT: C 285 ASN cc_start: 0.9396 (m110) cc_final: 0.9016 (m-40) REVERT: C 311 LYS cc_start: 0.9023 (tmtt) cc_final: 0.8484 (tptt) REVERT: C 379 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9166 (tm) REVERT: C 386 MET cc_start: 0.8950 (ppp) cc_final: 0.8339 (ppp) REVERT: C 407 ARG cc_start: 0.7343 (ttt180) cc_final: 0.6701 (ttt180) REVERT: C 482 MET cc_start: 0.8543 (tpt) cc_final: 0.8240 (tpt) REVERT: C 489 LYS cc_start: 0.8346 (ttmm) cc_final: 0.8123 (tptm) REVERT: C 490 PHE cc_start: 0.8065 (m-80) cc_final: 0.7795 (m-80) REVERT: C 509 TYR cc_start: 0.7646 (p90) cc_final: 0.7018 (p90) REVERT: C 514 PHE cc_start: 0.7356 (p90) cc_final: 0.6945 (p90) REVERT: D 91 ILE cc_start: 0.9103 (mm) cc_final: 0.8878 (mm) REVERT: D 128 ARG cc_start: 0.9040 (mmt90) cc_final: 0.8797 (mmm-85) REVERT: D 199 GLU cc_start: 0.9362 (tp30) cc_final: 0.9027 (tp30) REVERT: D 202 GLN cc_start: 0.9415 (mt0) cc_final: 0.8652 (mt0) REVERT: D 214 GLU cc_start: 0.9444 (mm-30) cc_final: 0.9205 (mp0) REVERT: D 216 ASP cc_start: 0.9054 (t70) cc_final: 0.8764 (t0) REVERT: D 284 ILE cc_start: 0.9437 (OUTLIER) cc_final: 0.9153 (mp) REVERT: D 285 ASN cc_start: 0.9320 (m110) cc_final: 0.8947 (m110) REVERT: D 311 LYS cc_start: 0.9078 (tmtt) cc_final: 0.8534 (tptt) REVERT: D 351 SER cc_start: 0.8939 (OUTLIER) cc_final: 0.8660 (t) REVERT: D 386 MET cc_start: 0.8845 (ppp) cc_final: 0.8204 (ppp) REVERT: D 407 ARG cc_start: 0.7443 (ttt180) cc_final: 0.6811 (ttt180) REVERT: D 420 MET cc_start: 0.6191 (tpp) cc_final: 0.5896 (mmm) REVERT: D 470 ASP cc_start: 0.8691 (m-30) cc_final: 0.8479 (m-30) REVERT: D 482 MET cc_start: 0.8579 (tpt) cc_final: 0.8244 (tpt) REVERT: D 490 PHE cc_start: 0.8246 (m-80) cc_final: 0.7878 (m-80) REVERT: D 509 TYR cc_start: 0.7723 (p90) cc_final: 0.7094 (p90) REVERT: D 514 PHE cc_start: 0.7418 (p90) cc_final: 0.7015 (p90) REVERT: E 52 THR cc_start: 0.9792 (m) cc_final: 0.9590 (t) REVERT: E 95 CYS cc_start: 0.8572 (p) cc_final: 0.8364 (p) REVERT: E 128 ARG cc_start: 0.8968 (mmt90) cc_final: 0.8702 (mmm-85) REVERT: E 199 GLU cc_start: 0.9406 (tp30) cc_final: 0.9072 (tp30) REVERT: E 206 LYS cc_start: 0.8076 (tppt) cc_final: 0.7633 (tppt) REVERT: E 214 GLU cc_start: 0.9401 (mm-30) cc_final: 0.9165 (mp0) REVERT: E 216 ASP cc_start: 0.9106 (t70) cc_final: 0.8847 (t0) REVERT: E 250 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7671 (pp) REVERT: E 285 ASN cc_start: 0.9391 (m110) cc_final: 0.9009 (m-40) REVERT: E 311 LYS cc_start: 0.9063 (tmtt) cc_final: 0.8563 (tptt) REVERT: E 386 MET cc_start: 0.8929 (ppp) cc_final: 0.8248 (ppp) REVERT: E 470 ASP cc_start: 0.8749 (m-30) cc_final: 0.8537 (m-30) REVERT: E 482 MET cc_start: 0.8560 (tpt) cc_final: 0.8273 (tpt) REVERT: E 490 PHE cc_start: 0.8215 (m-80) cc_final: 0.7916 (m-80) REVERT: E 509 TYR cc_start: 0.7810 (p90) cc_final: 0.7160 (p90) REVERT: F 91 ILE cc_start: 0.9027 (mm) cc_final: 0.8805 (mm) REVERT: F 109 LYS cc_start: 0.8830 (mmtm) cc_final: 0.8606 (mmtm) REVERT: F 128 ARG cc_start: 0.9007 (mmt90) cc_final: 0.8558 (mmt90) REVERT: F 170 GLU cc_start: 0.8537 (pt0) cc_final: 0.8199 (pt0) REVERT: F 194 LEU cc_start: 0.9524 (tp) cc_final: 0.9296 (tp) REVERT: F 199 GLU cc_start: 0.9385 (tp30) cc_final: 0.9057 (tp30) REVERT: F 216 ASP cc_start: 0.9053 (t70) cc_final: 0.8772 (t0) REVERT: F 284 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9251 (mp) REVERT: F 285 ASN cc_start: 0.9316 (m110) cc_final: 0.8937 (m110) REVERT: F 311 LYS cc_start: 0.9063 (tmtt) cc_final: 0.8537 (tptt) REVERT: F 386 MET cc_start: 0.8857 (ppp) cc_final: 0.8293 (ppp) REVERT: F 401 PHE cc_start: 0.8300 (p90) cc_final: 0.8068 (p90) REVERT: F 407 ARG cc_start: 0.7430 (ttt180) cc_final: 0.7163 (ttt90) REVERT: F 470 ASP cc_start: 0.8733 (m-30) cc_final: 0.8504 (m-30) REVERT: F 482 MET cc_start: 0.8602 (tpt) cc_final: 0.8275 (tpt) REVERT: F 490 PHE cc_start: 0.8233 (m-80) cc_final: 0.7849 (m-80) REVERT: F 509 TYR cc_start: 0.7861 (p90) cc_final: 0.7259 (p90) REVERT: F 514 PHE cc_start: 0.7391 (p90) cc_final: 0.7039 (p90) REVERT: G 32 TYR cc_start: 0.8706 (m-80) cc_final: 0.8486 (m-10) REVERT: G 98 GLU cc_start: 0.8858 (mp0) cc_final: 0.8651 (mp0) REVERT: G 128 ARG cc_start: 0.9032 (mmt90) cc_final: 0.8758 (mmm-85) REVERT: G 199 GLU cc_start: 0.9388 (tp30) cc_final: 0.9037 (tp30) REVERT: G 214 GLU cc_start: 0.9443 (mm-30) cc_final: 0.9204 (mp0) REVERT: G 250 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7845 (pp) REVERT: G 284 ILE cc_start: 0.9512 (OUTLIER) cc_final: 0.9266 (mp) REVERT: G 285 ASN cc_start: 0.9409 (m110) cc_final: 0.9042 (m-40) REVERT: G 311 LYS cc_start: 0.9071 (tmtt) cc_final: 0.8576 (tptt) REVERT: G 379 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9167 (tm) REVERT: G 386 MET cc_start: 0.8995 (ppp) cc_final: 0.8233 (ppp) REVERT: G 482 MET cc_start: 0.8617 (tpt) cc_final: 0.8303 (tpt) REVERT: G 490 PHE cc_start: 0.8282 (m-80) cc_final: 0.7998 (m-80) REVERT: G 509 TYR cc_start: 0.7860 (p90) cc_final: 0.7253 (p90) REVERT: H 18 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8664 (tm) REVERT: H 19 THR cc_start: 0.8725 (p) cc_final: 0.8246 (t) REVERT: H 91 ILE cc_start: 0.8996 (mm) cc_final: 0.8767 (mm) REVERT: H 128 ARG cc_start: 0.9049 (mmt90) cc_final: 0.8657 (mmt90) REVERT: H 170 GLU cc_start: 0.8361 (pt0) cc_final: 0.8062 (pt0) REVERT: H 180 THR cc_start: 0.8429 (p) cc_final: 0.8228 (t) REVERT: H 194 LEU cc_start: 0.9526 (tp) cc_final: 0.9306 (tp) REVERT: H 199 GLU cc_start: 0.9365 (tp30) cc_final: 0.9069 (tp30) REVERT: H 205 LYS cc_start: 0.9386 (mppt) cc_final: 0.9130 (mmtt) REVERT: H 216 ASP cc_start: 0.8981 (t70) cc_final: 0.8728 (t0) REVERT: H 284 ILE cc_start: 0.9484 (OUTLIER) cc_final: 0.9247 (mp) REVERT: H 285 ASN cc_start: 0.9389 (m110) cc_final: 0.8979 (m-40) REVERT: H 311 LYS cc_start: 0.8974 (tmtt) cc_final: 0.8412 (tptt) REVERT: H 351 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8668 (t) REVERT: H 386 MET cc_start: 0.8863 (ppp) cc_final: 0.8294 (ppp) REVERT: H 401 PHE cc_start: 0.8294 (p90) cc_final: 0.8034 (p90) REVERT: H 407 ARG cc_start: 0.7402 (ttt180) cc_final: 0.7099 (ttt90) REVERT: H 482 MET cc_start: 0.8478 (tpt) cc_final: 0.8160 (tpt) REVERT: H 489 LYS cc_start: 0.8418 (ttmm) cc_final: 0.8135 (tptm) REVERT: H 509 TYR cc_start: 0.7950 (p90) cc_final: 0.7369 (p90) outliers start: 384 outliers final: 165 residues processed: 1505 average time/residue: 0.1993 time to fit residues: 472.0107 Evaluate side-chains 1220 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 1033 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain D residue 487 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 449 ASP Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 487 GLU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 134 LYS Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 487 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 160 SER Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 449 ASP Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain G residue 487 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 134 LYS Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 469 GLN Chi-restraints excluded: chain H residue 487 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 0.0870 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.0020 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.2170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 ASN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 309 GLN D 368 GLN ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN ** G 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN ** H 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 GLN H 368 GLN H 498 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.166889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.129323 restraints weight = 50127.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.134923 restraints weight = 28641.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.138778 restraints weight = 19391.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.141596 restraints weight = 14530.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.143606 restraints weight = 11625.090| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31592 Z= 0.169 Angle : 0.848 10.026 42888 Z= 0.421 Chirality : 0.050 0.179 4888 Planarity : 0.005 0.040 5328 Dihedral : 21.552 162.316 5602 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 7.61 % Allowed : 23.06 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -3.13 (0.12), residues: 3880 helix: -2.18 (0.12), residues: 1224 sheet: -2.74 (0.18), residues: 520 loop : -1.79 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 149 TYR 0.023 0.002 TYR D 484 PHE 0.018 0.002 PHE B 456 HIS 0.005 0.001 HIS D 466 Details of bonding type rmsd covalent geometry : bond 0.00382 (31576) covalent geometry : angle 0.84827 (42888) hydrogen bonds : bond 0.04985 ( 832) hydrogen bonds : angle 6.06143 ( 2376) Misc. bond : bond 0.00066 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1326 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 243 poor density : 1083 time to evaluate : 1.199 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: 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 32 TYR cc_start: 0.8683 (m-80) cc_final: 0.8358 (m-10) REVERT: A 68 SER cc_start: 0.8821 (t) cc_final: 0.8603 (t) REVERT: A 70 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8234 (mtm) REVERT: A 73 VAL cc_start: 0.8279 (OUTLIER) cc_final: 0.6682 (t) REVERT: A 136 ARG cc_start: 0.8998 (ptp-110) cc_final: 0.8783 (ptp90) REVERT: A 165 PHE cc_start: 0.8242 (p90) cc_final: 0.8039 (p90) REVERT: A 202 GLN cc_start: 0.9297 (mt0) cc_final: 0.8892 (mt0) REVERT: A 205 LYS cc_start: 0.9177 (mppt) cc_final: 0.8916 (mttt) REVERT: A 206 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8015 (tptt) REVERT: A 250 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.7857 (pp) REVERT: A 254 GLU cc_start: 0.9331 (pp20) cc_final: 0.9127 (pm20) REVERT: A 273 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8559 (mm) REVERT: A 285 ASN cc_start: 0.9462 (m110) cc_final: 0.9141 (m110) REVERT: A 297 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8687 (tm) REVERT: A 311 LYS cc_start: 0.8739 (tmtt) cc_final: 0.8218 (tptt) REVERT: A 352 GLU cc_start: 0.8613 (tp30) cc_final: 0.8394 (tp30) REVERT: A 379 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9243 (tm) REVERT: A 386 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8377 (ppp) REVERT: A 407 ARG cc_start: 0.7424 (ttt180) cc_final: 0.7091 (ttt90) REVERT: A 420 MET cc_start: 0.6566 (mmm) cc_final: 0.6076 (mmm) REVERT: A 470 ASP cc_start: 0.8495 (m-30) cc_final: 0.8098 (m-30) REVERT: A 482 MET cc_start: 0.8502 (tpt) cc_final: 0.8129 (tpt) REVERT: A 487 GLU cc_start: 0.8538 (pm20) cc_final: 0.8047 (pm20) REVERT: A 490 PHE cc_start: 0.8260 (m-80) cc_final: 0.7892 (m-80) REVERT: A 509 TYR cc_start: 0.7764 (p90) cc_final: 0.7490 (p90) REVERT: A 510 GLU cc_start: 0.6654 (mm-30) cc_final: 0.6450 (mm-30) REVERT: A 514 PHE cc_start: 0.7193 (p90) cc_final: 0.6483 (p90) REVERT: B 161 ARG cc_start: 0.9525 (mpp-170) cc_final: 0.9066 (mtt90) REVERT: B 165 PHE cc_start: 0.7995 (p90) cc_final: 0.7729 (p90) REVERT: B 180 THR cc_start: 0.8169 (p) cc_final: 0.7812 (t) REVERT: B 199 GLU cc_start: 0.9312 (tp30) cc_final: 0.8913 (tp30) REVERT: B 202 GLN cc_start: 0.9328 (mt0) cc_final: 0.8979 (mt0) REVERT: B 203 ARG cc_start: 0.9019 (ptp-110) cc_final: 0.8811 (ptp-110) REVERT: B 206 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8158 (ttpt) REVERT: B 208 LYS cc_start: 0.8338 (mtpp) cc_final: 0.8098 (ttmm) REVERT: B 216 ASP cc_start: 0.8948 (t70) cc_final: 0.8608 (t0) REVERT: B 232 ASP cc_start: 0.9271 (t0) cc_final: 0.9038 (t0) REVERT: B 233 TYR cc_start: 0.8992 (m-80) cc_final: 0.8719 (m-80) REVERT: B 258 TYR cc_start: 0.8354 (t80) cc_final: 0.8055 (t80) REVERT: B 285 ASN cc_start: 0.9360 (m110) cc_final: 0.9115 (m110) REVERT: B 297 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8723 (tm) REVERT: B 311 LYS cc_start: 0.8891 (tmtt) cc_final: 0.8315 (tptt) REVERT: B 385 MET cc_start: 0.8598 (ttp) cc_final: 0.8373 (ttp) REVERT: B 386 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8305 (ppp) REVERT: B 399 GLU cc_start: 0.7263 (pp20) cc_final: 0.7013 (pp20) REVERT: B 400 TYR cc_start: 0.7889 (m-80) cc_final: 0.7427 (m-80) REVERT: B 401 PHE cc_start: 0.8276 (p90) cc_final: 0.8050 (p90) REVERT: B 482 MET cc_start: 0.8500 (tpt) cc_final: 0.8151 (tpt) REVERT: B 487 GLU cc_start: 0.8539 (pm20) cc_final: 0.8173 (pm20) REVERT: B 490 PHE cc_start: 0.8400 (m-80) cc_final: 0.7971 (m-80) REVERT: B 514 PHE cc_start: 0.7156 (p90) cc_final: 0.6909 (p90) REVERT: C 32 TYR cc_start: 0.8666 (m-80) cc_final: 0.8381 (m-10) REVERT: C 78 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7974 (ttp) REVERT: C 199 GLU cc_start: 0.9324 (tp30) cc_final: 0.9024 (tp30) REVERT: C 202 GLN cc_start: 0.9335 (mt0) cc_final: 0.8939 (mt0) REVERT: C 206 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8086 (ttpt) REVERT: C 208 LYS cc_start: 0.8461 (mtpp) cc_final: 0.8215 (ttmm) REVERT: C 250 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7543 (pp) REVERT: C 261 ASP cc_start: 0.8879 (m-30) cc_final: 0.8637 (p0) REVERT: C 285 ASN cc_start: 0.9387 (m110) cc_final: 0.9075 (m110) REVERT: C 297 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8686 (tm) REVERT: C 311 LYS cc_start: 0.8819 (tmtt) cc_final: 0.8346 (tptt) REVERT: C 357 PHE cc_start: 0.8862 (m-80) cc_final: 0.8507 (m-10) REVERT: C 386 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8404 (ppp) REVERT: C 407 ARG cc_start: 0.7411 (ttt180) cc_final: 0.6819 (ttt90) REVERT: C 420 MET cc_start: 0.6431 (mmm) cc_final: 0.5995 (mmm) REVERT: C 466 HIS cc_start: 0.9039 (OUTLIER) cc_final: 0.8254 (t-90) REVERT: C 470 ASP cc_start: 0.8518 (m-30) cc_final: 0.8066 (m-30) REVERT: C 482 MET cc_start: 0.8557 (tpt) cc_final: 0.8216 (tpt) REVERT: C 487 GLU cc_start: 0.8592 (pm20) cc_final: 0.8219 (pm20) REVERT: C 490 PHE cc_start: 0.8301 (m-80) cc_final: 0.7931 (m-80) REVERT: C 514 PHE cc_start: 0.7218 (p90) cc_final: 0.6977 (p90) REVERT: D 32 TYR cc_start: 0.8614 (m-10) cc_final: 0.8394 (m-10) REVERT: D 73 VAL cc_start: 0.8154 (OUTLIER) cc_final: 0.6384 (t) REVERT: D 78 MET cc_start: 0.8358 (ttm) cc_final: 0.8021 (ttp) REVERT: D 161 ARG cc_start: 0.9550 (mpp-170) cc_final: 0.9055 (mtt90) REVERT: D 165 PHE cc_start: 0.8008 (p90) cc_final: 0.7738 (p90) REVERT: D 180 THR cc_start: 0.8453 (p) cc_final: 0.8053 (t) REVERT: D 199 GLU cc_start: 0.9506 (tp30) cc_final: 0.9216 (tp30) REVERT: D 206 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8017 (ttpt) REVERT: D 216 ASP cc_start: 0.8977 (t70) cc_final: 0.8645 (t0) REVERT: D 233 TYR cc_start: 0.9005 (m-80) cc_final: 0.8742 (m-80) REVERT: D 273 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8495 (mm) REVERT: D 297 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8780 (tm) REVERT: D 311 LYS cc_start: 0.8888 (tmtt) cc_final: 0.8454 (tptt) REVERT: D 385 MET cc_start: 0.8634 (ttp) cc_final: 0.8352 (ttp) REVERT: D 386 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8316 (ppp) REVERT: D 399 GLU cc_start: 0.7305 (pp20) cc_final: 0.7097 (pp20) REVERT: D 407 ARG cc_start: 0.7469 (ttt180) cc_final: 0.7210 (ttt180) REVERT: D 461 ILE cc_start: 0.9099 (pp) cc_final: 0.8666 (pt) REVERT: D 482 MET cc_start: 0.8580 (tpt) cc_final: 0.8209 (tpt) REVERT: D 484 TYR cc_start: 0.9063 (m-10) cc_final: 0.8156 (m-10) REVERT: D 487 GLU cc_start: 0.8580 (pm20) cc_final: 0.8209 (pm20) REVERT: D 490 PHE cc_start: 0.8354 (m-80) cc_final: 0.7951 (m-80) REVERT: E 32 TYR cc_start: 0.8625 (m-10) cc_final: 0.8359 (m-10) REVERT: E 78 MET cc_start: 0.8455 (ttm) cc_final: 0.8234 (ttt) REVERT: E 165 PHE cc_start: 0.8131 (p90) cc_final: 0.7695 (p90) REVERT: E 185 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7589 (mt) REVERT: E 199 GLU cc_start: 0.9528 (tp30) cc_final: 0.9260 (tp30) REVERT: E 206 LYS cc_start: 0.7997 (tppt) cc_final: 0.7667 (tppt) REVERT: E 216 ASP cc_start: 0.9016 (t70) cc_final: 0.8662 (t0) REVERT: E 250 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7570 (pp) REVERT: E 285 ASN cc_start: 0.9335 (m110) cc_final: 0.9034 (m110) REVERT: E 297 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8685 (tm) REVERT: E 311 LYS cc_start: 0.8858 (tmtt) cc_final: 0.8430 (tptt) REVERT: E 379 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9228 (tm) REVERT: E 385 MET cc_start: 0.8528 (ttp) cc_final: 0.8096 (ttp) REVERT: E 386 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8318 (ppp) REVERT: E 420 MET cc_start: 0.6498 (mmm) cc_final: 0.6109 (mmm) REVERT: E 482 MET cc_start: 0.8543 (tpt) cc_final: 0.8212 (tpt) REVERT: E 487 GLU cc_start: 0.8611 (pm20) cc_final: 0.8247 (pm20) REVERT: E 490 PHE cc_start: 0.8411 (m-80) cc_final: 0.8054 (m-80) REVERT: F 78 MET cc_start: 0.8460 (ttm) cc_final: 0.8233 (ttt) REVERT: F 109 LYS cc_start: 0.8657 (mmtm) cc_final: 0.8399 (mmtm) REVERT: F 161 ARG cc_start: 0.9436 (mpp-170) cc_final: 0.8463 (mtt90) REVERT: F 165 PHE cc_start: 0.8165 (p90) cc_final: 0.7642 (p90) REVERT: F 180 THR cc_start: 0.8237 (p) cc_final: 0.7909 (t) REVERT: F 199 GLU cc_start: 0.9514 (tp30) cc_final: 0.9200 (tp30) REVERT: F 203 ARG cc_start: 0.9334 (ptp-110) cc_final: 0.9127 (ptp-110) REVERT: F 206 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8094 (ttpt) REVERT: F 216 ASP cc_start: 0.9013 (t70) cc_final: 0.8674 (t0) REVERT: F 258 TYR cc_start: 0.8371 (t80) cc_final: 0.8035 (t80) REVERT: F 265 GLN cc_start: 0.9245 (mm110) cc_final: 0.9032 (mm-40) REVERT: F 297 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8717 (tm) REVERT: F 311 LYS cc_start: 0.8855 (tmtt) cc_final: 0.8428 (tptt) REVERT: F 386 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8239 (ppp) REVERT: F 400 TYR cc_start: 0.7936 (m-80) cc_final: 0.7396 (m-80) REVERT: F 401 PHE cc_start: 0.8273 (p90) cc_final: 0.8009 (p90) REVERT: F 466 HIS cc_start: 0.9080 (OUTLIER) cc_final: 0.8281 (t-90) REVERT: F 470 ASP cc_start: 0.8741 (m-30) cc_final: 0.8540 (m-30) REVERT: F 482 MET cc_start: 0.8585 (tpt) cc_final: 0.8249 (tpt) REVERT: F 487 GLU cc_start: 0.8652 (pm20) cc_final: 0.8284 (pm20) REVERT: F 490 PHE cc_start: 0.8446 (m-80) cc_final: 0.8015 (m-80) REVERT: F 514 PHE cc_start: 0.7277 (p90) cc_final: 0.7005 (p90) REVERT: G 32 TYR cc_start: 0.8632 (m-80) cc_final: 0.8404 (m-10) REVERT: G 73 VAL cc_start: 0.8372 (OUTLIER) cc_final: 0.6793 (t) REVERT: G 78 MET cc_start: 0.8420 (ttm) cc_final: 0.8213 (ttp) REVERT: G 109 LYS cc_start: 0.8761 (mmtm) cc_final: 0.8499 (mmtm) REVERT: G 165 PHE cc_start: 0.8081 (p90) cc_final: 0.7839 (p90) REVERT: G 179 MET cc_start: 0.7766 (ptm) cc_final: 0.7506 (ptt) REVERT: G 199 GLU cc_start: 0.9526 (tp30) cc_final: 0.9136 (tp30) REVERT: G 206 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7985 (ttpt) REVERT: G 285 ASN cc_start: 0.9389 (m110) cc_final: 0.9059 (m110) REVERT: G 297 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8732 (tm) REVERT: G 311 LYS cc_start: 0.8847 (tmtt) cc_final: 0.8423 (tptt) REVERT: G 379 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9256 (tm) REVERT: G 385 MET cc_start: 0.8463 (ttp) cc_final: 0.8050 (ttt) REVERT: G 386 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8320 (ppp) REVERT: G 420 MET cc_start: 0.6519 (mmm) cc_final: 0.6120 (mmm) REVERT: G 466 HIS cc_start: 0.9075 (OUTLIER) cc_final: 0.8304 (t-90) REVERT: G 470 ASP cc_start: 0.8466 (m-30) cc_final: 0.8037 (m-30) REVERT: G 482 MET cc_start: 0.8575 (tpt) cc_final: 0.8231 (tpt) REVERT: G 487 GLU cc_start: 0.8645 (pm20) cc_final: 0.8286 (pm20) REVERT: G 490 PHE cc_start: 0.8411 (m-80) cc_final: 0.8062 (m-80) REVERT: H 32 TYR cc_start: 0.8588 (m-10) cc_final: 0.7969 (m-10) REVERT: H 136 ARG cc_start: 0.9025 (ptp-110) cc_final: 0.8694 (ptp90) REVERT: H 165 PHE cc_start: 0.8104 (p90) cc_final: 0.7608 (p90) REVERT: H 180 THR cc_start: 0.8214 (p) cc_final: 0.7938 (t) REVERT: H 199 GLU cc_start: 0.9454 (tp30) cc_final: 0.9210 (tp30) REVERT: H 206 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8069 (ttmm) REVERT: H 216 ASP cc_start: 0.8828 (t70) cc_final: 0.8469 (t0) REVERT: H 273 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8569 (mm) REVERT: H 297 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8691 (tm) REVERT: H 311 LYS cc_start: 0.8805 (tmtt) cc_final: 0.8372 (tptt) REVERT: H 379 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9181 (tm) REVERT: H 386 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8189 (pmm) REVERT: H 390 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8716 (tt) REVERT: H 400 TYR cc_start: 0.7828 (m-80) cc_final: 0.7416 (m-80) REVERT: H 401 PHE cc_start: 0.8263 (p90) cc_final: 0.8026 (p90) REVERT: H 441 GLN cc_start: 0.8549 (mm-40) cc_final: 0.8318 (mm-40) REVERT: H 482 MET cc_start: 0.8501 (tpt) cc_final: 0.8131 (tpt) REVERT: H 484 TYR cc_start: 0.9019 (m-10) cc_final: 0.8202 (m-10) REVERT: H 487 GLU cc_start: 0.8616 (pm20) cc_final: 0.8211 (pm20) REVERT: H 490 PHE cc_start: 0.8276 (m-80) cc_final: 0.7901 (m-80) REVERT: H 514 PHE cc_start: 0.7258 (p90) cc_final: 0.6982 (p90) outliers start: 243 outliers final: 115 residues processed: 1178 average time/residue: 0.1876 time to fit residues: 357.3571 Evaluate side-chains 1076 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 918 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 466 HIS Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 466 HIS Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 466 HIS Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 469 GLN Chi-restraints excluded: chain H residue 498 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 206 optimal weight: 20.0000 chunk 74 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 59 optimal weight: 20.0000 chunk 275 optimal weight: 0.0870 chunk 225 optimal weight: 0.4980 chunk 171 optimal weight: 2.9990 chunk 299 optimal weight: 20.0000 chunk 325 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 overall best weight: 2.7164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN A 283 GLN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN A 498 GLN ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 283 GLN B 303 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN D 283 GLN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN E 243 GLN E 303 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN ** F 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN ** G 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 GLN ** H 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN H 283 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.159856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.122089 restraints weight = 51512.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.127320 restraints weight = 30018.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.131017 restraints weight = 20702.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.133608 restraints weight = 15722.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.135560 restraints weight = 12771.640| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 31592 Z= 0.217 Angle : 0.831 14.448 42888 Z= 0.411 Chirality : 0.050 0.162 4888 Planarity : 0.005 0.050 5328 Dihedral : 20.232 178.541 5381 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 8.99 % Allowed : 24.50 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -2.55 (0.13), residues: 3880 helix: -1.83 (0.13), residues: 1296 sheet: -2.34 (0.19), residues: 512 loop : -1.33 (0.14), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 149 TYR 0.030 0.002 TYR H 233 PHE 0.018 0.002 PHE F 90 HIS 0.006 0.001 HIS H 454 Details of bonding type rmsd covalent geometry : bond 0.00483 (31576) covalent geometry : angle 0.83126 (42888) hydrogen bonds : bond 0.04253 ( 832) hydrogen bonds : angle 5.74818 ( 2376) Misc. bond : bond 0.00034 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1336 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 287 poor density : 1049 time to evaluate : 1.134 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: 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 32 TYR cc_start: 0.8600 (m-80) cc_final: 0.8325 (m-10) REVERT: A 165 PHE cc_start: 0.8131 (p90) cc_final: 0.7871 (p90) REVERT: A 202 GLN cc_start: 0.9397 (mt0) cc_final: 0.8855 (mt0) REVERT: A 206 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7866 (ttpt) REVERT: A 250 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7826 (pp) REVERT: A 254 GLU cc_start: 0.9350 (pp20) cc_final: 0.9079 (pm20) REVERT: A 285 ASN cc_start: 0.9456 (m110) cc_final: 0.9125 (m110) REVERT: A 297 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8810 (tm) REVERT: A 311 LYS cc_start: 0.8853 (tmtt) cc_final: 0.7993 (tppt) REVERT: A 337 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7200 (tt) REVERT: A 348 TYR cc_start: 0.9186 (t80) cc_final: 0.8830 (t80) REVERT: A 379 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9242 (tm) REVERT: A 386 MET cc_start: 0.9084 (ppp) cc_final: 0.8203 (ppp) REVERT: A 469 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.7824 (pt0) REVERT: A 470 ASP cc_start: 0.8581 (m-30) cc_final: 0.8302 (m-30) REVERT: A 482 MET cc_start: 0.8652 (tpt) cc_final: 0.8407 (tpt) REVERT: A 487 GLU cc_start: 0.8410 (pm20) cc_final: 0.7955 (pm20) REVERT: A 488 LEU cc_start: 0.8511 (tm) cc_final: 0.8257 (tm) REVERT: A 490 PHE cc_start: 0.8313 (m-80) cc_final: 0.8065 (m-80) REVERT: A 510 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6535 (mm-30) REVERT: B 65 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9027 (pt) REVERT: B 128 ARG cc_start: 0.8791 (mmt90) cc_final: 0.8589 (mmm-85) REVERT: B 161 ARG cc_start: 0.9413 (mpp-170) cc_final: 0.9191 (mpp80) REVERT: B 165 PHE cc_start: 0.7972 (p90) cc_final: 0.7747 (p90) REVERT: B 176 GLU cc_start: 0.9166 (mp0) cc_final: 0.8895 (mp0) REVERT: B 199 GLU cc_start: 0.9296 (tp30) cc_final: 0.8965 (tp30) REVERT: B 202 GLN cc_start: 0.9286 (mt0) cc_final: 0.8921 (mt0) REVERT: B 206 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8080 (ttpt) REVERT: B 216 ASP cc_start: 0.9009 (t70) cc_final: 0.8646 (t0) REVERT: B 250 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7783 (pp) REVERT: B 265 GLN cc_start: 0.9256 (mm110) cc_final: 0.9043 (mm-40) REVERT: B 311 LYS cc_start: 0.8962 (tmtt) cc_final: 0.8451 (tptt) REVERT: B 337 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7269 (tt) REVERT: B 385 MET cc_start: 0.8625 (ttp) cc_final: 0.8417 (ttp) REVERT: B 386 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8198 (pmm) REVERT: B 407 ARG cc_start: 0.7400 (ttt180) cc_final: 0.7098 (ttt90) REVERT: B 420 MET cc_start: 0.6842 (mmm) cc_final: 0.6441 (mmm) REVERT: B 470 ASP cc_start: 0.8567 (m-30) cc_final: 0.8149 (m-30) REVERT: B 482 MET cc_start: 0.8597 (tpt) cc_final: 0.8266 (tpt) REVERT: B 487 GLU cc_start: 0.8605 (pm20) cc_final: 0.8291 (pm20) REVERT: B 490 PHE cc_start: 0.8372 (m-80) cc_final: 0.7915 (m-80) REVERT: B 509 TYR cc_start: 0.7811 (p90) cc_final: 0.7598 (p90) REVERT: C 32 TYR cc_start: 0.8627 (m-80) cc_final: 0.8343 (m-10) REVERT: C 73 VAL cc_start: 0.8450 (OUTLIER) cc_final: 0.6817 (t) REVERT: C 128 ARG cc_start: 0.8828 (mmt90) cc_final: 0.8550 (mmt90) REVERT: C 176 GLU cc_start: 0.9236 (mp0) cc_final: 0.8973 (mp0) REVERT: C 199 GLU cc_start: 0.9480 (tp30) cc_final: 0.9182 (tp30) REVERT: C 206 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7977 (ttpt) REVERT: C 208 LYS cc_start: 0.8646 (mtpp) cc_final: 0.8407 (ttmm) REVERT: C 216 ASP cc_start: 0.9065 (t70) cc_final: 0.8698 (t0) REVERT: C 235 LEU cc_start: 0.9149 (mt) cc_final: 0.8941 (mt) REVERT: C 250 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7759 (pp) REVERT: C 261 ASP cc_start: 0.8769 (m-30) cc_final: 0.8452 (p0) REVERT: C 265 GLN cc_start: 0.9276 (mm110) cc_final: 0.9055 (mm-40) REVERT: C 297 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8777 (tm) REVERT: C 311 LYS cc_start: 0.8823 (tmtt) cc_final: 0.7955 (tppt) REVERT: C 337 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7131 (tt) REVERT: C 386 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8086 (ppp) REVERT: C 420 MET cc_start: 0.6619 (mmm) cc_final: 0.6182 (mmm) REVERT: C 470 ASP cc_start: 0.8614 (m-30) cc_final: 0.8263 (m-30) REVERT: C 482 MET cc_start: 0.8684 (tpt) cc_final: 0.8453 (tpt) REVERT: C 487 GLU cc_start: 0.8538 (pm20) cc_final: 0.8106 (pm20) REVERT: C 490 PHE cc_start: 0.8422 (m-80) cc_final: 0.8118 (m-80) REVERT: C 509 TYR cc_start: 0.7684 (p90) cc_final: 0.7387 (p90) REVERT: C 510 GLU cc_start: 0.6784 (mm-30) cc_final: 0.6421 (mm-30) REVERT: C 514 PHE cc_start: 0.7423 (p90) cc_final: 0.7186 (p90) REVERT: D 73 VAL cc_start: 0.8228 (OUTLIER) cc_final: 0.6595 (t) REVERT: D 78 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7871 (ttt) REVERT: D 128 ARG cc_start: 0.8822 (mmt90) cc_final: 0.8560 (ttm-80) REVERT: D 161 ARG cc_start: 0.9422 (mpp-170) cc_final: 0.9171 (mpp80) REVERT: D 165 PHE cc_start: 0.8005 (p90) cc_final: 0.7779 (p90) REVERT: D 176 GLU cc_start: 0.9207 (mp0) cc_final: 0.8940 (mp0) REVERT: D 199 GLU cc_start: 0.9490 (tp30) cc_final: 0.9202 (tp30) REVERT: D 206 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8053 (ttpt) REVERT: D 216 ASP cc_start: 0.9035 (t70) cc_final: 0.8686 (t0) REVERT: D 297 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8893 (tm) REVERT: D 311 LYS cc_start: 0.8935 (tmtt) cc_final: 0.8416 (tptt) REVERT: D 337 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7292 (tt) REVERT: D 386 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8483 (pmm) REVERT: D 390 LEU cc_start: 0.9093 (tt) cc_final: 0.8590 (tt) REVERT: D 400 TYR cc_start: 0.7815 (m-80) cc_final: 0.7536 (m-80) REVERT: D 407 ARG cc_start: 0.7394 (ttt180) cc_final: 0.7116 (ttt180) REVERT: D 420 MET cc_start: 0.6759 (mmm) cc_final: 0.6338 (mmm) REVERT: D 470 ASP cc_start: 0.8679 (m-30) cc_final: 0.8261 (m-30) REVERT: D 482 MET cc_start: 0.8615 (tpt) cc_final: 0.8359 (tpt) REVERT: D 487 GLU cc_start: 0.8565 (pm20) cc_final: 0.8133 (pm20) REVERT: D 490 PHE cc_start: 0.8407 (m-80) cc_final: 0.7995 (m-80) REVERT: D 509 TYR cc_start: 0.7723 (p90) cc_final: 0.7505 (p90) REVERT: D 510 GLU cc_start: 0.6780 (mm-30) cc_final: 0.6565 (mm-30) REVERT: D 514 PHE cc_start: 0.7443 (p90) cc_final: 0.7115 (p90) REVERT: E 78 MET cc_start: 0.8470 (ttm) cc_final: 0.8105 (ttt) REVERT: E 128 ARG cc_start: 0.8785 (mmt90) cc_final: 0.8515 (mmt90) REVERT: E 165 PHE cc_start: 0.8133 (p90) cc_final: 0.7626 (p90) REVERT: E 176 GLU cc_start: 0.9214 (mp0) cc_final: 0.8953 (mp0) REVERT: E 185 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7590 (mt) REVERT: E 206 LYS cc_start: 0.8250 (tppt) cc_final: 0.7891 (tppt) REVERT: E 216 ASP cc_start: 0.9065 (t70) cc_final: 0.8711 (t0) REVERT: E 235 LEU cc_start: 0.9156 (mt) cc_final: 0.8935 (mt) REVERT: E 250 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7799 (pp) REVERT: E 261 ASP cc_start: 0.8835 (m-30) cc_final: 0.8492 (p0) REVERT: E 297 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8823 (tm) REVERT: E 311 LYS cc_start: 0.8924 (tmtt) cc_final: 0.8479 (tptt) REVERT: E 337 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7124 (tt) REVERT: E 352 GLU cc_start: 0.8838 (tp30) cc_final: 0.8627 (tp30) REVERT: E 379 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9250 (tm) REVERT: E 385 MET cc_start: 0.8419 (ttp) cc_final: 0.8042 (ttp) REVERT: E 386 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8239 (ppp) REVERT: E 420 MET cc_start: 0.6760 (mmm) cc_final: 0.6362 (mmm) REVERT: E 469 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.7835 (pt0) REVERT: E 470 ASP cc_start: 0.8717 (m-30) cc_final: 0.8286 (m-30) REVERT: E 482 MET cc_start: 0.8587 (tpt) cc_final: 0.8379 (tpt) REVERT: E 487 GLU cc_start: 0.8633 (pm20) cc_final: 0.8223 (pm20) REVERT: E 490 PHE cc_start: 0.8376 (m-80) cc_final: 0.8013 (m-80) REVERT: E 509 TYR cc_start: 0.7867 (p90) cc_final: 0.7552 (p90) REVERT: E 510 GLU cc_start: 0.6802 (mm-30) cc_final: 0.6398 (mm-30) REVERT: F 62 LYS cc_start: 0.9281 (mmtp) cc_final: 0.8821 (mttm) REVERT: F 78 MET cc_start: 0.8526 (ttm) cc_final: 0.8134 (ttt) REVERT: F 165 PHE cc_start: 0.8186 (p90) cc_final: 0.7590 (p90) REVERT: F 176 GLU cc_start: 0.9189 (mp0) cc_final: 0.8926 (mp0) REVERT: F 199 GLU cc_start: 0.9505 (tp30) cc_final: 0.9148 (tp30) REVERT: F 206 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8051 (ttpt) REVERT: F 216 ASP cc_start: 0.9054 (t70) cc_final: 0.8692 (t0) REVERT: F 235 LEU cc_start: 0.9152 (mt) cc_final: 0.8558 (mt) REVERT: F 250 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7721 (pp) REVERT: F 265 GLN cc_start: 0.9282 (mm110) cc_final: 0.9047 (mm-40) REVERT: F 297 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8902 (tm) REVERT: F 311 LYS cc_start: 0.8911 (tmtt) cc_final: 0.8429 (tptt) REVERT: F 337 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7159 (tt) REVERT: F 352 GLU cc_start: 0.8813 (tp30) cc_final: 0.8588 (tp30) REVERT: F 379 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9231 (tm) REVERT: F 386 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8336 (ppp) REVERT: F 482 MET cc_start: 0.8624 (tpt) cc_final: 0.8315 (tpt) REVERT: F 487 GLU cc_start: 0.8684 (pm20) cc_final: 0.8367 (pm20) REVERT: F 490 PHE cc_start: 0.8399 (m-80) cc_final: 0.7909 (m-80) REVERT: F 509 TYR cc_start: 0.7838 (p90) cc_final: 0.7611 (p90) REVERT: F 510 GLU cc_start: 0.6648 (mm-30) cc_final: 0.6421 (mm-30) REVERT: F 514 PHE cc_start: 0.7483 (p90) cc_final: 0.7164 (p90) REVERT: G 32 TYR cc_start: 0.8608 (m-80) cc_final: 0.8387 (m-10) REVERT: G 73 VAL cc_start: 0.8587 (OUTLIER) cc_final: 0.6936 (t) REVERT: G 78 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8233 (ttp) REVERT: G 165 PHE cc_start: 0.8066 (p90) cc_final: 0.7820 (p90) REVERT: G 199 GLU cc_start: 0.9475 (tp30) cc_final: 0.9162 (tp30) REVERT: G 206 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8076 (ttpt) REVERT: G 250 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.7986 (pp) REVERT: G 258 TYR cc_start: 0.8597 (t80) cc_final: 0.8387 (t80) REVERT: G 297 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8888 (tm) REVERT: G 311 LYS cc_start: 0.8913 (tmtt) cc_final: 0.8083 (tppt) REVERT: G 337 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7442 (tt) REVERT: G 379 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.9314 (tm) REVERT: G 385 MET cc_start: 0.8360 (ttp) cc_final: 0.7940 (ttp) REVERT: G 386 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8238 (ppp) REVERT: G 407 ARG cc_start: 0.7368 (ttt180) cc_final: 0.6812 (ttt90) REVERT: G 441 GLN cc_start: 0.8418 (mm-40) cc_final: 0.8200 (mm-40) REVERT: G 470 ASP cc_start: 0.8595 (m-30) cc_final: 0.8362 (m-30) REVERT: G 482 MET cc_start: 0.8651 (tpt) cc_final: 0.8307 (tpt) REVERT: G 487 GLU cc_start: 0.8689 (pm20) cc_final: 0.8378 (pm20) REVERT: G 490 PHE cc_start: 0.8355 (m-80) cc_final: 0.8017 (m-80) REVERT: G 509 TYR cc_start: 0.7873 (p90) cc_final: 0.7529 (p90) REVERT: G 510 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6655 (mm-30) REVERT: H 32 TYR cc_start: 0.8350 (m-10) cc_final: 0.8050 (m-10) REVERT: H 62 LYS cc_start: 0.9314 (mmtp) cc_final: 0.8819 (mttm) REVERT: H 65 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9035 (pt) REVERT: H 66 VAL cc_start: 0.8922 (OUTLIER) cc_final: 0.8584 (p) REVERT: H 73 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.7032 (t) REVERT: H 136 ARG cc_start: 0.8996 (ptp-110) cc_final: 0.8728 (ptp90) REVERT: H 161 ARG cc_start: 0.9550 (mpp-170) cc_final: 0.9343 (mpp80) REVERT: H 165 PHE cc_start: 0.8094 (p90) cc_final: 0.7814 (p90) REVERT: H 199 GLU cc_start: 0.9478 (tp30) cc_final: 0.9231 (tp30) REVERT: H 206 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7994 (ttpt) REVERT: H 216 ASP cc_start: 0.8954 (t70) cc_final: 0.8629 (t0) REVERT: H 235 LEU cc_start: 0.9154 (mt) cc_final: 0.8498 (mt) REVERT: H 243 GLN cc_start: 0.8575 (mp-120) cc_final: 0.8243 (mp10) REVERT: H 250 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.7989 (pp) REVERT: H 283 GLN cc_start: 0.8715 (tt0) cc_final: 0.8509 (mt0) REVERT: H 297 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8867 (tm) REVERT: H 311 LYS cc_start: 0.8902 (tmtt) cc_final: 0.8404 (tptt) REVERT: H 337 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7346 (tt) REVERT: H 379 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9158 (tm) REVERT: H 386 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8139 (pmm) REVERT: H 400 TYR cc_start: 0.7845 (m-80) cc_final: 0.7210 (m-80) REVERT: H 401 PHE cc_start: 0.8259 (p90) cc_final: 0.7930 (p90) REVERT: H 470 ASP cc_start: 0.8725 (m-30) cc_final: 0.8317 (m-30) REVERT: H 482 MET cc_start: 0.8565 (tpt) cc_final: 0.8306 (tpt) REVERT: H 487 GLU cc_start: 0.8542 (pm20) cc_final: 0.8113 (pm20) REVERT: H 490 PHE cc_start: 0.8304 (m-80) cc_final: 0.7869 (m-80) REVERT: H 509 TYR cc_start: 0.7978 (p90) cc_final: 0.7700 (p90) REVERT: H 514 PHE cc_start: 0.7523 (p90) cc_final: 0.7175 (p90) outliers start: 287 outliers final: 168 residues processed: 1181 average time/residue: 0.1921 time to fit residues: 365.7883 Evaluate side-chains 1180 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 958 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 294 TYR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 498 GLN Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 222 ILE Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 345 THR Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 355 ARG Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 469 GLN Chi-restraints excluded: chain H residue 494 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 219 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 237 optimal weight: 0.9980 chunk 185 optimal weight: 0.0670 chunk 323 optimal weight: 1.9990 chunk 304 optimal weight: 7.9990 chunk 282 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 chunk 169 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 133 optimal weight: 5.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS A 309 GLN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 303 ASN B 309 GLN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN C 171 HIS ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 GLN C 309 GLN ** C 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 GLN C 498 GLN D 171 HIS ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN E 171 HIS ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN E 465 GLN E 498 GLN F 171 HIS ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 GLN ** F 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 GLN ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 465 GLN G 171 HIS ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 309 GLN ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN H 171 HIS ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.165674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.128818 restraints weight = 50179.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.134388 restraints weight = 28611.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.138294 restraints weight = 19361.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.141099 restraints weight = 14439.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.143034 restraints weight = 11515.799| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31592 Z= 0.142 Angle : 0.804 13.367 42888 Z= 0.384 Chirality : 0.048 0.179 4888 Planarity : 0.005 0.084 5328 Dihedral : 18.489 152.300 5366 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 8.99 % Allowed : 26.38 % Favored : 64.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -2.40 (0.13), residues: 3880 helix: -1.63 (0.13), residues: 1296 sheet: -2.55 (0.20), residues: 472 loop : -1.25 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 182 TYR 0.032 0.002 TYR A 233 PHE 0.011 0.001 PHE H 90 HIS 0.004 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00320 (31576) covalent geometry : angle 0.80413 (42888) hydrogen bonds : bond 0.03709 ( 832) hydrogen bonds : angle 5.50699 ( 2376) Misc. bond : bond 0.00039 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1359 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 287 poor density : 1072 time to evaluate : 1.158 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: 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 32 TYR cc_start: 0.8500 (m-80) cc_final: 0.8256 (m-10) REVERT: A 51 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8045 (pp) REVERT: A 66 VAL cc_start: 0.9004 (OUTLIER) cc_final: 0.8664 (p) REVERT: A 128 ARG cc_start: 0.8835 (mmt90) cc_final: 0.8541 (mmt90) REVERT: A 165 PHE cc_start: 0.8049 (p90) cc_final: 0.7819 (p90) REVERT: A 206 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7875 (ttpt) REVERT: A 230 ASN cc_start: 0.8605 (t0) cc_final: 0.8123 (t0) REVERT: A 250 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7755 (pp) REVERT: A 285 ASN cc_start: 0.9448 (m110) cc_final: 0.9133 (m110) REVERT: A 297 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8744 (tm) REVERT: A 311 LYS cc_start: 0.8736 (tmtt) cc_final: 0.7824 (tppt) REVERT: A 337 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7141 (tt) REVERT: A 355 ARG cc_start: 0.8793 (ttm170) cc_final: 0.8535 (ttm170) REVERT: A 379 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9222 (tm) REVERT: A 386 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8153 (pmm) REVERT: A 469 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.7801 (pt0) REVERT: A 470 ASP cc_start: 0.8628 (m-30) cc_final: 0.8265 (m-30) REVERT: A 482 MET cc_start: 0.8651 (tpt) cc_final: 0.8416 (tpt) REVERT: A 487 GLU cc_start: 0.8393 (pm20) cc_final: 0.7975 (pm20) REVERT: A 490 PHE cc_start: 0.8272 (m-80) cc_final: 0.8030 (m-80) REVERT: A 509 TYR cc_start: 0.7614 (p90) cc_final: 0.7062 (p90) REVERT: A 510 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6718 (mm-30) REVERT: B 109 LYS cc_start: 0.8724 (mmtm) cc_final: 0.8377 (mptt) REVERT: B 161 ARG cc_start: 0.9428 (mpp-170) cc_final: 0.9121 (mtt90) REVERT: B 206 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7992 (ttpt) REVERT: B 216 ASP cc_start: 0.8956 (t70) cc_final: 0.8568 (t0) REVERT: B 261 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8339 (p0) REVERT: B 283 GLN cc_start: 0.8705 (tt0) cc_final: 0.8442 (mt0) REVERT: B 311 LYS cc_start: 0.8912 (tmtt) cc_final: 0.8383 (tptt) REVERT: B 337 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7238 (tt) REVERT: B 386 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8385 (pmm) REVERT: B 407 ARG cc_start: 0.7525 (ttt180) cc_final: 0.7265 (ttt180) REVERT: B 420 MET cc_start: 0.6886 (mmm) cc_final: 0.6524 (mmm) REVERT: B 465 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7912 (mt0) REVERT: B 469 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.7624 (pt0) REVERT: B 470 ASP cc_start: 0.8662 (m-30) cc_final: 0.8280 (m-30) REVERT: B 482 MET cc_start: 0.8590 (tpt) cc_final: 0.8266 (tpt) REVERT: B 487 GLU cc_start: 0.8496 (pm20) cc_final: 0.8260 (pm20) REVERT: B 490 PHE cc_start: 0.8289 (m-80) cc_final: 0.7894 (m-80) REVERT: B 509 TYR cc_start: 0.7811 (p90) cc_final: 0.7555 (p90) REVERT: C 32 TYR cc_start: 0.8558 (m-80) cc_final: 0.8343 (m-10) REVERT: C 109 LYS cc_start: 0.8734 (mmtm) cc_final: 0.8466 (mptt) REVERT: C 199 GLU cc_start: 0.9469 (tp30) cc_final: 0.9182 (tp30) REVERT: C 203 ARG cc_start: 0.9369 (ptp-110) cc_final: 0.9134 (ptp-110) REVERT: C 206 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7925 (ttpt) REVERT: C 208 LYS cc_start: 0.8671 (mtpp) cc_final: 0.8104 (mtpp) REVERT: C 214 GLU cc_start: 0.9274 (mm-30) cc_final: 0.9060 (mp0) REVERT: C 235 LEU cc_start: 0.9066 (mt) cc_final: 0.8850 (mt) REVERT: C 250 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7549 (pp) REVERT: C 258 TYR cc_start: 0.8515 (t80) cc_final: 0.8173 (t80) REVERT: C 262 LEU cc_start: 0.9386 (tp) cc_final: 0.9158 (tp) REVERT: C 297 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8768 (tm) REVERT: C 311 LYS cc_start: 0.8786 (tmtt) cc_final: 0.7906 (tppt) REVERT: C 337 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7266 (tt) REVERT: C 348 TYR cc_start: 0.9299 (t80) cc_final: 0.8921 (t80) REVERT: C 386 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8360 (ppp) REVERT: C 400 TYR cc_start: 0.7521 (m-80) cc_final: 0.7189 (m-80) REVERT: C 407 ARG cc_start: 0.7254 (ttt180) cc_final: 0.6793 (ttt90) REVERT: C 420 MET cc_start: 0.6699 (mmm) cc_final: 0.6318 (mmm) REVERT: C 470 ASP cc_start: 0.8626 (m-30) cc_final: 0.8283 (m-30) REVERT: C 482 MET cc_start: 0.8633 (tpt) cc_final: 0.8411 (tpt) REVERT: C 487 GLU cc_start: 0.8405 (pm20) cc_final: 0.8096 (pm20) REVERT: C 490 PHE cc_start: 0.8378 (m-80) cc_final: 0.8128 (m-80) REVERT: C 509 TYR cc_start: 0.7718 (p90) cc_final: 0.7395 (p90) REVERT: C 510 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6666 (mm-30) REVERT: D 73 VAL cc_start: 0.8054 (OUTLIER) cc_final: 0.6643 (t) REVERT: D 161 ARG cc_start: 0.9462 (mpp-170) cc_final: 0.9142 (mpp80) REVERT: D 165 PHE cc_start: 0.7933 (p90) cc_final: 0.7707 (p90) REVERT: D 199 GLU cc_start: 0.9447 (tp30) cc_final: 0.9227 (tp30) REVERT: D 206 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8014 (ttpt) REVERT: D 216 ASP cc_start: 0.9011 (t70) cc_final: 0.8626 (t0) REVERT: D 297 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8857 (tm) REVERT: D 311 LYS cc_start: 0.8844 (tmtt) cc_final: 0.8298 (tptt) REVERT: D 337 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7241 (tt) REVERT: D 386 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8270 (pmm) REVERT: D 390 LEU cc_start: 0.8994 (tt) cc_final: 0.8541 (tt) REVERT: D 400 TYR cc_start: 0.7783 (m-80) cc_final: 0.7406 (m-80) REVERT: D 407 ARG cc_start: 0.7374 (ttt180) cc_final: 0.6639 (ttt180) REVERT: D 420 MET cc_start: 0.6726 (mmm) cc_final: 0.6396 (mmm) REVERT: D 469 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.7805 (pt0) REVERT: D 470 ASP cc_start: 0.8737 (m-30) cc_final: 0.8245 (m-30) REVERT: D 482 MET cc_start: 0.8604 (tpt) cc_final: 0.8344 (tpt) REVERT: D 487 GLU cc_start: 0.8476 (pm20) cc_final: 0.8105 (pm20) REVERT: D 490 PHE cc_start: 0.8331 (m-80) cc_final: 0.7860 (m-80) REVERT: D 509 TYR cc_start: 0.7777 (p90) cc_final: 0.7551 (p90) REVERT: E 65 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9035 (pt) REVERT: E 78 MET cc_start: 0.8168 (ttm) cc_final: 0.7879 (ttt) REVERT: E 109 LYS cc_start: 0.8789 (mmtm) cc_final: 0.8385 (mptt) REVERT: E 128 ARG cc_start: 0.8793 (mmt90) cc_final: 0.8485 (mmt90) REVERT: E 165 PHE cc_start: 0.8057 (p90) cc_final: 0.7825 (p90) REVERT: E 185 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7796 (mt) REVERT: E 203 ARG cc_start: 0.9292 (ptp-110) cc_final: 0.9082 (ptp-110) REVERT: E 206 LYS cc_start: 0.8137 (tppt) cc_final: 0.7797 (tppt) REVERT: E 216 ASP cc_start: 0.9092 (t70) cc_final: 0.8734 (t0) REVERT: E 235 LEU cc_start: 0.9049 (mt) cc_final: 0.8820 (mt) REVERT: E 250 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7713 (pp) REVERT: E 257 LYS cc_start: 0.8935 (mttt) cc_final: 0.8727 (mttp) REVERT: E 297 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8730 (tm) REVERT: E 311 LYS cc_start: 0.8884 (tmtt) cc_final: 0.8442 (tptt) REVERT: E 337 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7138 (tt) REVERT: E 348 TYR cc_start: 0.9292 (t80) cc_final: 0.8986 (t80) REVERT: E 379 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9198 (tm) REVERT: E 386 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8288 (ppp) REVERT: E 400 TYR cc_start: 0.7608 (m-80) cc_final: 0.7321 (m-80) REVERT: E 407 ARG cc_start: 0.7310 (ttt180) cc_final: 0.5960 (ttt180) REVERT: E 420 MET cc_start: 0.6759 (mmm) cc_final: 0.6440 (mmm) REVERT: E 469 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.7674 (pt0) REVERT: E 470 ASP cc_start: 0.8670 (m-30) cc_final: 0.8287 (m-30) REVERT: E 482 MET cc_start: 0.8566 (tpt) cc_final: 0.8357 (tpt) REVERT: E 487 GLU cc_start: 0.8517 (pm20) cc_final: 0.8174 (pm20) REVERT: E 488 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7928 (tm) REVERT: E 490 PHE cc_start: 0.8372 (m-80) cc_final: 0.8058 (m-80) REVERT: E 509 TYR cc_start: 0.7813 (p90) cc_final: 0.7424 (p90) REVERT: E 510 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6639 (mm-30) REVERT: F 62 LYS cc_start: 0.9235 (mmtp) cc_final: 0.8730 (mttm) REVERT: F 78 MET cc_start: 0.8388 (ttm) cc_final: 0.8007 (ttt) REVERT: F 132 GLU cc_start: 0.9462 (mp0) cc_final: 0.9227 (mp0) REVERT: F 165 PHE cc_start: 0.8214 (p90) cc_final: 0.7905 (p90) REVERT: F 166 LEU cc_start: 0.8173 (tp) cc_final: 0.7906 (tp) REVERT: F 199 GLU cc_start: 0.9492 (tp30) cc_final: 0.9245 (tp30) REVERT: F 206 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7983 (ttpt) REVERT: F 216 ASP cc_start: 0.8986 (t70) cc_final: 0.8608 (t0) REVERT: F 235 LEU cc_start: 0.9040 (mt) cc_final: 0.8388 (mt) REVERT: F 261 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8257 (p0) REVERT: F 297 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8822 (tm) REVERT: F 309 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8804 (pt0) REVERT: F 311 LYS cc_start: 0.8892 (tmtt) cc_final: 0.8380 (tptt) REVERT: F 337 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7279 (tt) REVERT: F 352 GLU cc_start: 0.8865 (tp30) cc_final: 0.8590 (tp30) REVERT: F 386 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8196 (pmm) REVERT: F 399 GLU cc_start: 0.8755 (pm20) cc_final: 0.8146 (tt0) REVERT: F 407 ARG cc_start: 0.7553 (ttt180) cc_final: 0.7141 (ttt90) REVERT: F 465 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7895 (mt0) REVERT: F 469 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.7692 (pt0) REVERT: F 470 ASP cc_start: 0.8711 (m-30) cc_final: 0.8271 (m-30) REVERT: F 482 MET cc_start: 0.8682 (tpt) cc_final: 0.8395 (tpt) REVERT: F 487 GLU cc_start: 0.8578 (pm20) cc_final: 0.8321 (pm20) REVERT: F 490 PHE cc_start: 0.8379 (m-80) cc_final: 0.7966 (m-80) REVERT: F 509 TYR cc_start: 0.7847 (p90) cc_final: 0.7603 (p90) REVERT: F 510 GLU cc_start: 0.6840 (mm-30) cc_final: 0.6628 (mm-30) REVERT: F 514 PHE cc_start: 0.7347 (p90) cc_final: 0.7015 (p90) REVERT: G 32 TYR cc_start: 0.8535 (m-80) cc_final: 0.8256 (m-10) REVERT: G 65 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9025 (pt) REVERT: G 109 LYS cc_start: 0.8823 (mmtm) cc_final: 0.8501 (mptt) REVERT: G 161 ARG cc_start: 0.9458 (mpp-170) cc_final: 0.8822 (mtt90) REVERT: G 203 ARG cc_start: 0.9379 (ptp-110) cc_final: 0.9171 (ptp-110) REVERT: G 206 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7959 (ttpt) REVERT: G 297 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8773 (tm) REVERT: G 311 LYS cc_start: 0.8804 (tmtt) cc_final: 0.7987 (tppt) REVERT: G 337 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7123 (tt) REVERT: G 379 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9252 (tm) REVERT: G 386 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8377 (pmm) REVERT: G 407 ARG cc_start: 0.7530 (ttt180) cc_final: 0.6798 (ttt-90) REVERT: G 420 MET cc_start: 0.6766 (mmm) cc_final: 0.6446 (mmm) REVERT: G 469 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.7807 (pt0) REVERT: G 470 ASP cc_start: 0.8662 (m-30) cc_final: 0.8280 (m-30) REVERT: G 482 MET cc_start: 0.8633 (tpt) cc_final: 0.8410 (tpt) REVERT: G 487 GLU cc_start: 0.8567 (pm20) cc_final: 0.8212 (pm20) REVERT: G 489 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7970 (tttt) REVERT: G 490 PHE cc_start: 0.8410 (m-80) cc_final: 0.8087 (m-80) REVERT: G 509 TYR cc_start: 0.7961 (p90) cc_final: 0.7602 (p90) REVERT: H 62 LYS cc_start: 0.9267 (mmtp) cc_final: 0.8752 (mttm) REVERT: H 78 MET cc_start: 0.7789 (ttt) cc_final: 0.7432 (ttt) REVERT: H 90 PHE cc_start: 0.8414 (m-10) cc_final: 0.8167 (m-10) REVERT: H 109 LYS cc_start: 0.8792 (mmtm) cc_final: 0.8345 (mptt) REVERT: H 161 ARG cc_start: 0.9474 (mpp-170) cc_final: 0.9228 (mpp80) REVERT: H 165 PHE cc_start: 0.7981 (p90) cc_final: 0.7744 (p90) REVERT: H 199 GLU cc_start: 0.9469 (tp30) cc_final: 0.9225 (tp30) REVERT: H 206 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7867 (ttpt) REVERT: H 216 ASP cc_start: 0.8918 (t70) cc_final: 0.8566 (t0) REVERT: H 235 LEU cc_start: 0.9053 (mt) cc_final: 0.8369 (mt) REVERT: H 265 GLN cc_start: 0.9298 (mm110) cc_final: 0.9045 (mm-40) REVERT: H 297 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8826 (tm) REVERT: H 309 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8806 (pt0) REVERT: H 311 LYS cc_start: 0.8848 (tmtt) cc_final: 0.8336 (tptt) REVERT: H 337 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7209 (tt) REVERT: H 386 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8103 (pmm) REVERT: H 401 PHE cc_start: 0.8243 (p90) cc_final: 0.7908 (p90) REVERT: H 465 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7852 (mt0) REVERT: H 469 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.7739 (pt0) REVERT: H 470 ASP cc_start: 0.8760 (m-30) cc_final: 0.8291 (m-30) REVERT: H 482 MET cc_start: 0.8581 (tpt) cc_final: 0.8266 (tpt) REVERT: H 487 GLU cc_start: 0.8521 (pm20) cc_final: 0.8234 (pm20) REVERT: H 490 PHE cc_start: 0.8197 (m-80) cc_final: 0.7789 (m-80) REVERT: H 509 TYR cc_start: 0.7999 (p90) cc_final: 0.7735 (p90) outliers start: 287 outliers final: 160 residues processed: 1212 average time/residue: 0.2045 time to fit residues: 395.2521 Evaluate side-chains 1205 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 986 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 498 GLN Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 294 TYR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 309 GLN Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 465 GLN Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain G residue 498 GLN Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 222 ILE Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 355 ARG Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain H residue 465 GLN Chi-restraints excluded: chain H residue 469 GLN Chi-restraints excluded: chain H residue 494 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 104 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 225 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 343 optimal weight: 7.9990 chunk 290 optimal weight: 1.9990 chunk 197 optimal weight: 0.0060 chunk 18 optimal weight: 4.9990 chunk 282 optimal weight: 3.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** 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 = 0.4224 r_free = 0.4224 target = 0.166816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.129725 restraints weight = 51284.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.135271 restraints weight = 29723.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.139184 restraints weight = 20274.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.141867 restraints weight = 15194.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.143950 restraints weight = 12207.280| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31592 Z= 0.144 Angle : 0.820 12.856 42888 Z= 0.390 Chirality : 0.049 0.237 4888 Planarity : 0.005 0.062 5328 Dihedral : 17.089 147.115 5354 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 8.36 % Allowed : 27.94 % Favored : 63.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -2.22 (0.13), residues: 3880 helix: -1.44 (0.13), residues: 1248 sheet: -2.24 (0.20), residues: 520 loop : -1.21 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 182 TYR 0.027 0.002 TYR C 233 PHE 0.021 0.001 PHE E 90 HIS 0.003 0.001 HIS H 454 Details of bonding type rmsd covalent geometry : bond 0.00331 (31576) covalent geometry : angle 0.81986 (42888) hydrogen bonds : bond 0.03620 ( 832) hydrogen bonds : angle 5.45361 ( 2376) Misc. bond : bond 0.00030 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1334 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 267 poor density : 1067 time to evaluate : 1.125 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: 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 32 TYR cc_start: 0.8519 (m-80) cc_final: 0.8306 (m-10) REVERT: A 51 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8007 (pp) REVERT: A 66 VAL cc_start: 0.9118 (OUTLIER) cc_final: 0.8890 (p) REVERT: A 109 LYS cc_start: 0.8858 (mmtm) cc_final: 0.8536 (mptt) REVERT: A 128 ARG cc_start: 0.8838 (mmt90) cc_final: 0.8537 (mmt90) REVERT: A 161 ARG cc_start: 0.9403 (mpp-170) cc_final: 0.9199 (mtt90) REVERT: A 165 PHE cc_start: 0.8073 (p90) cc_final: 0.7804 (p90) REVERT: A 186 VAL cc_start: 0.9397 (m) cc_final: 0.9102 (m) REVERT: A 206 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7737 (ttpt) REVERT: A 230 ASN cc_start: 0.8566 (t0) cc_final: 0.7993 (t0) REVERT: A 231 ARG cc_start: 0.8986 (ttp-110) cc_final: 0.8779 (ttp80) REVERT: A 250 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7696 (pp) REVERT: A 285 ASN cc_start: 0.9463 (m110) cc_final: 0.9151 (m110) REVERT: A 297 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8695 (tm) REVERT: A 311 LYS cc_start: 0.8747 (tmtt) cc_final: 0.7839 (tppt) REVERT: A 337 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7205 (tt) REVERT: A 352 GLU cc_start: 0.8728 (tp30) cc_final: 0.8396 (tp30) REVERT: A 379 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9180 (tm) REVERT: A 386 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8195 (pmm) REVERT: A 470 ASP cc_start: 0.8573 (m-30) cc_final: 0.8320 (m-30) REVERT: A 482 MET cc_start: 0.8623 (tpt) cc_final: 0.8359 (tpt) REVERT: A 487 GLU cc_start: 0.8339 (pm20) cc_final: 0.7948 (pm20) REVERT: A 490 PHE cc_start: 0.8308 (m-80) cc_final: 0.8075 (m-80) REVERT: A 509 TYR cc_start: 0.7690 (p90) cc_final: 0.7192 (p90) REVERT: A 510 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6680 (mm-30) REVERT: B 109 LYS cc_start: 0.8779 (mmtm) cc_final: 0.8475 (mptt) REVERT: B 186 VAL cc_start: 0.9370 (OUTLIER) cc_final: 0.9164 (m) REVERT: B 206 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7954 (ttpt) REVERT: B 216 ASP cc_start: 0.8979 (t70) cc_final: 0.8597 (t0) REVERT: B 258 TYR cc_start: 0.7970 (t80) cc_final: 0.7768 (t80) REVERT: B 261 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8290 (p0) REVERT: B 283 GLN cc_start: 0.8742 (tt0) cc_final: 0.8496 (mt0) REVERT: B 311 LYS cc_start: 0.8905 (tmtt) cc_final: 0.7957 (tppt) REVERT: B 337 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7274 (tt) REVERT: B 386 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8359 (pmm) REVERT: B 407 ARG cc_start: 0.7529 (ttt180) cc_final: 0.7193 (ttt90) REVERT: B 420 MET cc_start: 0.6762 (mmm) cc_final: 0.6453 (mmm) REVERT: B 469 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.7642 (pt0) REVERT: B 470 ASP cc_start: 0.8679 (m-30) cc_final: 0.8365 (m-30) REVERT: B 482 MET cc_start: 0.8653 (tpt) cc_final: 0.8325 (tpt) REVERT: B 490 PHE cc_start: 0.8332 (m-80) cc_final: 0.8026 (m-80) REVERT: C 109 LYS cc_start: 0.8791 (mmtm) cc_final: 0.8506 (mptt) REVERT: C 132 GLU cc_start: 0.9442 (mp0) cc_final: 0.9132 (mp0) REVERT: C 199 GLU cc_start: 0.9500 (tp30) cc_final: 0.9280 (tp30) REVERT: C 203 ARG cc_start: 0.9345 (ptp-110) cc_final: 0.9137 (ptp-110) REVERT: C 206 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7940 (ttpt) REVERT: C 208 LYS cc_start: 0.8696 (mtpp) cc_final: 0.7860 (mtpp) REVERT: C 243 GLN cc_start: 0.8375 (mp-120) cc_final: 0.8169 (mp10) REVERT: C 250 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7640 (pp) REVERT: C 297 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8721 (tm) REVERT: C 311 LYS cc_start: 0.8741 (tmtt) cc_final: 0.7836 (tppt) REVERT: C 337 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7248 (tt) REVERT: C 386 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8259 (pmm) REVERT: C 420 MET cc_start: 0.6769 (mmm) cc_final: 0.6386 (mmm) REVERT: C 465 GLN cc_start: 0.8009 (pt0) cc_final: 0.7545 (mt0) REVERT: C 469 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.7819 (pt0) REVERT: C 470 ASP cc_start: 0.8565 (m-30) cc_final: 0.8198 (m-30) REVERT: C 482 MET cc_start: 0.8627 (tpt) cc_final: 0.8402 (tpt) REVERT: C 487 GLU cc_start: 0.8365 (pm20) cc_final: 0.7979 (pm20) REVERT: C 490 PHE cc_start: 0.8412 (m-80) cc_final: 0.8152 (m-80) REVERT: C 509 TYR cc_start: 0.7794 (p90) cc_final: 0.7521 (p90) REVERT: C 510 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6741 (mm-30) REVERT: D 73 VAL cc_start: 0.8101 (OUTLIER) cc_final: 0.7557 (t) REVERT: D 78 MET cc_start: 0.7640 (ttt) cc_final: 0.7270 (tmm) REVERT: D 165 PHE cc_start: 0.7947 (p90) cc_final: 0.7743 (p90) REVERT: D 199 GLU cc_start: 0.9445 (tp30) cc_final: 0.8835 (tp30) REVERT: D 203 ARG cc_start: 0.9373 (ptp-110) cc_final: 0.8718 (mtm-85) REVERT: D 216 ASP cc_start: 0.8985 (t70) cc_final: 0.8615 (t0) REVERT: D 265 GLN cc_start: 0.9258 (mm110) cc_final: 0.9038 (mm-40) REVERT: D 297 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8823 (tm) REVERT: D 311 LYS cc_start: 0.8821 (tmtt) cc_final: 0.7858 (tppt) REVERT: D 337 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7287 (tt) REVERT: D 386 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8244 (pmm) REVERT: D 400 TYR cc_start: 0.7795 (m-80) cc_final: 0.7379 (m-80) REVERT: D 407 ARG cc_start: 0.7408 (ttt180) cc_final: 0.6596 (ttt180) REVERT: D 420 MET cc_start: 0.6657 (mmm) cc_final: 0.6339 (mmm) REVERT: D 469 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7770 (pt0) REVERT: D 470 ASP cc_start: 0.8702 (m-30) cc_final: 0.8333 (m-30) REVERT: D 482 MET cc_start: 0.8578 (tpt) cc_final: 0.8306 (tpt) REVERT: D 487 GLU cc_start: 0.8439 (pm20) cc_final: 0.8154 (pm20) REVERT: D 488 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7707 (tp) REVERT: D 490 PHE cc_start: 0.8365 (m-80) cc_final: 0.7972 (m-80) REVERT: E 78 MET cc_start: 0.8240 (ttm) cc_final: 0.7944 (ttt) REVERT: E 109 LYS cc_start: 0.8846 (mmtm) cc_final: 0.8573 (mptt) REVERT: E 128 ARG cc_start: 0.8785 (mmt90) cc_final: 0.8491 (mmt90) REVERT: E 132 GLU cc_start: 0.9464 (mp0) cc_final: 0.9155 (mp0) REVERT: E 161 ARG cc_start: 0.9424 (mpp-170) cc_final: 0.9017 (mtm-85) REVERT: E 165 PHE cc_start: 0.8068 (p90) cc_final: 0.7860 (p90) REVERT: E 185 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7918 (mt) REVERT: E 206 LYS cc_start: 0.8056 (tppt) cc_final: 0.7811 (tppt) REVERT: E 216 ASP cc_start: 0.9109 (t70) cc_final: 0.8763 (t0) REVERT: E 235 LEU cc_start: 0.9022 (mt) cc_final: 0.8810 (mt) REVERT: E 250 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7737 (pp) REVERT: E 297 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8670 (tm) REVERT: E 311 LYS cc_start: 0.8846 (tmtt) cc_final: 0.7885 (tppt) REVERT: E 337 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7149 (tt) REVERT: E 348 TYR cc_start: 0.9275 (t80) cc_final: 0.8974 (t80) REVERT: E 379 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9176 (tm) REVERT: E 386 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8337 (ppp) REVERT: E 400 TYR cc_start: 0.7550 (m-80) cc_final: 0.7348 (m-80) REVERT: E 407 ARG cc_start: 0.7329 (ttt180) cc_final: 0.6673 (tpt-90) REVERT: E 420 MET cc_start: 0.6835 (mmm) cc_final: 0.6504 (mmm) REVERT: E 469 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.7685 (pt0) REVERT: E 470 ASP cc_start: 0.8636 (m-30) cc_final: 0.8340 (m-30) REVERT: E 482 MET cc_start: 0.8628 (tpt) cc_final: 0.8400 (tpt) REVERT: E 487 GLU cc_start: 0.8394 (pm20) cc_final: 0.7999 (pm20) REVERT: E 488 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8037 (tm) REVERT: E 509 TYR cc_start: 0.7908 (p90) cc_final: 0.7560 (p90) REVERT: E 510 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6665 (mm-30) REVERT: F 62 LYS cc_start: 0.9240 (mmtp) cc_final: 0.8732 (mttm) REVERT: F 78 MET cc_start: 0.8273 (ttm) cc_final: 0.7910 (ttt) REVERT: F 109 LYS cc_start: 0.8564 (mmtm) cc_final: 0.8078 (mptt) REVERT: F 132 GLU cc_start: 0.9483 (mp0) cc_final: 0.9214 (mp0) REVERT: F 165 PHE cc_start: 0.8283 (p90) cc_final: 0.7983 (p90) REVERT: F 166 LEU cc_start: 0.8171 (tp) cc_final: 0.7886 (tp) REVERT: F 206 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7941 (ttpt) REVERT: F 216 ASP cc_start: 0.9002 (t70) cc_final: 0.8632 (t0) REVERT: F 235 LEU cc_start: 0.9017 (mt) cc_final: 0.8405 (mt) REVERT: F 261 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8277 (p0) REVERT: F 283 GLN cc_start: 0.8676 (tt0) cc_final: 0.8427 (mt0) REVERT: F 297 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8767 (tm) REVERT: F 311 LYS cc_start: 0.8821 (tmtt) cc_final: 0.7888 (tppt) REVERT: F 337 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7360 (tt) REVERT: F 352 GLU cc_start: 0.8799 (tp30) cc_final: 0.8557 (tp30) REVERT: F 386 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8246 (pmm) REVERT: F 399 GLU cc_start: 0.8667 (pm20) cc_final: 0.8147 (tt0) REVERT: F 407 ARG cc_start: 0.7561 (ttt180) cc_final: 0.7177 (ttt90) REVERT: F 408 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8619 (mp) REVERT: F 469 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7648 (pt0) REVERT: F 470 ASP cc_start: 0.8674 (m-30) cc_final: 0.8332 (m-30) REVERT: F 482 MET cc_start: 0.8677 (tpt) cc_final: 0.8376 (tpt) REVERT: F 490 PHE cc_start: 0.8405 (m-80) cc_final: 0.8139 (m-80) REVERT: F 510 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6671 (mm-30) REVERT: G 32 TYR cc_start: 0.8565 (m-80) cc_final: 0.8300 (m-10) REVERT: G 65 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9056 (pt) REVERT: G 73 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.7047 (t) REVERT: G 74 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8318 (p) REVERT: G 109 LYS cc_start: 0.8844 (mmtm) cc_final: 0.8584 (mptt) REVERT: G 132 GLU cc_start: 0.9451 (mp0) cc_final: 0.9144 (mp0) REVERT: G 161 ARG cc_start: 0.9451 (mpp-170) cc_final: 0.8831 (mtt90) REVERT: G 165 PHE cc_start: 0.8025 (p90) cc_final: 0.7706 (p90) REVERT: G 206 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7875 (ttpt) REVERT: G 208 LYS cc_start: 0.8212 (ttmm) cc_final: 0.7953 (ttmm) REVERT: G 289 TYR cc_start: 0.8869 (t80) cc_final: 0.8477 (t80) REVERT: G 297 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8715 (tm) REVERT: G 311 LYS cc_start: 0.8757 (tmtt) cc_final: 0.7948 (tppt) REVERT: G 337 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7233 (tt) REVERT: G 379 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9157 (tm) REVERT: G 386 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8367 (pmm) REVERT: G 407 ARG cc_start: 0.7561 (ttt180) cc_final: 0.7310 (ttt180) REVERT: G 420 MET cc_start: 0.6652 (mmm) cc_final: 0.6309 (mmm) REVERT: G 470 ASP cc_start: 0.8637 (m-30) cc_final: 0.8355 (m-30) REVERT: G 482 MET cc_start: 0.8678 (tpt) cc_final: 0.8434 (tpt) REVERT: G 487 GLU cc_start: 0.8505 (pm20) cc_final: 0.8131 (pm20) REVERT: G 489 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7950 (tttt) REVERT: G 490 PHE cc_start: 0.8399 (m-80) cc_final: 0.8100 (m-80) REVERT: G 509 TYR cc_start: 0.7997 (p90) cc_final: 0.7645 (p90) REVERT: H 62 LYS cc_start: 0.9241 (mmtp) cc_final: 0.8791 (mttm) REVERT: H 109 LYS cc_start: 0.8773 (mmtm) cc_final: 0.8421 (mptt) REVERT: H 161 ARG cc_start: 0.9423 (mpp-170) cc_final: 0.8878 (mtt90) REVERT: H 165 PHE cc_start: 0.8001 (p90) cc_final: 0.7756 (p90) REVERT: H 199 GLU cc_start: 0.9456 (tp30) cc_final: 0.9195 (tp30) REVERT: H 202 GLN cc_start: 0.9260 (mm-40) cc_final: 0.8811 (mm-40) REVERT: H 206 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7765 (ttpt) REVERT: H 216 ASP cc_start: 0.8942 (t70) cc_final: 0.8626 (t0) REVERT: H 235 LEU cc_start: 0.9043 (mt) cc_final: 0.8380 (mt) REVERT: H 297 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8773 (tm) REVERT: H 309 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8683 (pt0) REVERT: H 311 LYS cc_start: 0.8849 (tmtt) cc_final: 0.7879 (tppt) REVERT: H 337 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7188 (tt) REVERT: H 386 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8154 (pmm) REVERT: H 401 PHE cc_start: 0.8268 (p90) cc_final: 0.7902 (p90) REVERT: H 470 ASP cc_start: 0.8751 (m-30) cc_final: 0.8406 (m-30) REVERT: H 482 MET cc_start: 0.8605 (tpt) cc_final: 0.8353 (tpt) REVERT: H 487 GLU cc_start: 0.8424 (pm20) cc_final: 0.8001 (pm20) REVERT: H 490 PHE cc_start: 0.8374 (m-80) cc_final: 0.8078 (m-80) REVERT: H 509 TYR cc_start: 0.8036 (p90) cc_final: 0.7799 (p90) outliers start: 267 outliers final: 166 residues processed: 1179 average time/residue: 0.2023 time to fit residues: 380.5559 Evaluate side-chains 1203 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 979 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 294 TYR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 222 ILE Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 355 ARG Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain H residue 469 GLN Chi-restraints excluded: chain H residue 494 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 374 optimal weight: 3.9990 chunk 362 optimal weight: 5.9990 chunk 269 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 chunk 358 optimal weight: 0.4980 chunk 63 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 274 optimal weight: 0.8980 chunk 250 optimal weight: 6.9990 chunk 219 optimal weight: 1.9990 chunk 350 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 HIS ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 GLN ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN F 283 GLN F 303 ASN F 368 GLN ** F 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 GLN H 465 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.163127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.125610 restraints weight = 51665.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.131005 restraints weight = 30233.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.134738 restraints weight = 20785.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.137415 restraints weight = 15768.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.139326 restraints weight = 12757.454| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31592 Z= 0.183 Angle : 0.832 11.522 42888 Z= 0.403 Chirality : 0.050 0.236 4888 Planarity : 0.005 0.079 5328 Dihedral : 16.289 143.675 5340 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 8.80 % Allowed : 29.48 % Favored : 61.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -2.14 (0.13), residues: 3880 helix: -1.42 (0.14), residues: 1240 sheet: -2.40 (0.21), residues: 512 loop : -1.07 (0.14), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 161 TYR 0.039 0.002 TYR C 233 PHE 0.025 0.001 PHE G 90 HIS 0.006 0.001 HIS F 466 Details of bonding type rmsd covalent geometry : bond 0.00418 (31576) covalent geometry : angle 0.83165 (42888) hydrogen bonds : bond 0.03517 ( 832) hydrogen bonds : angle 5.41703 ( 2376) Misc. bond : bond 0.00058 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1314 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 281 poor density : 1033 time to evaluate : 1.148 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: 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 51 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8086 (pp) REVERT: A 66 VAL cc_start: 0.9098 (OUTLIER) cc_final: 0.8853 (p) REVERT: A 78 MET cc_start: 0.7345 (ttp) cc_final: 0.6960 (tmm) REVERT: A 109 LYS cc_start: 0.8901 (mmtm) cc_final: 0.8608 (mppt) REVERT: A 128 ARG cc_start: 0.8848 (mmt90) cc_final: 0.8556 (mmt90) REVERT: A 165 PHE cc_start: 0.8033 (p90) cc_final: 0.7730 (p90) REVERT: A 250 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.7940 (pp) REVERT: A 261 ASP cc_start: 0.8896 (m-30) cc_final: 0.8692 (t0) REVERT: A 297 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8748 (tm) REVERT: A 311 LYS cc_start: 0.8712 (tmtt) cc_final: 0.8276 (tmtt) REVERT: A 379 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9206 (tm) REVERT: A 386 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8489 (pmm) REVERT: A 470 ASP cc_start: 0.8633 (m-30) cc_final: 0.8358 (m-30) REVERT: A 482 MET cc_start: 0.8767 (tpt) cc_final: 0.8461 (tpt) REVERT: A 487 GLU cc_start: 0.8300 (pm20) cc_final: 0.7902 (pm20) REVERT: A 490 PHE cc_start: 0.8379 (m-80) cc_final: 0.8108 (m-80) REVERT: A 509 TYR cc_start: 0.7742 (p90) cc_final: 0.7368 (p90) REVERT: A 510 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6774 (mm-30) REVERT: B 32 TYR cc_start: 0.8432 (m-10) cc_final: 0.8207 (m-10) REVERT: B 109 LYS cc_start: 0.8804 (mmtm) cc_final: 0.8480 (mptt) REVERT: B 216 ASP cc_start: 0.9040 (t70) cc_final: 0.8670 (t0) REVERT: B 261 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8351 (p0) REVERT: B 311 LYS cc_start: 0.8805 (tmtt) cc_final: 0.7887 (tppt) REVERT: B 337 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7269 (tt) REVERT: B 355 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8366 (ttm110) REVERT: B 386 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8445 (pmm) REVERT: B 420 MET cc_start: 0.7215 (mmm) cc_final: 0.6845 (mmm) REVERT: B 469 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7900 (pt0) REVERT: B 482 MET cc_start: 0.8669 (tpt) cc_final: 0.8221 (tpt) REVERT: B 487 GLU cc_start: 0.8336 (pm20) cc_final: 0.7240 (pm20) REVERT: B 490 PHE cc_start: 0.8421 (m-80) cc_final: 0.8134 (m-80) REVERT: B 509 TYR cc_start: 0.7420 (p90) cc_final: 0.7054 (p90) REVERT: C 109 LYS cc_start: 0.8792 (mmtm) cc_final: 0.8469 (mptt) REVERT: C 128 ARG cc_start: 0.8781 (mmt90) cc_final: 0.8515 (mmt90) REVERT: C 132 GLU cc_start: 0.9425 (mp0) cc_final: 0.9107 (mp0) REVERT: C 150 MET cc_start: 0.9034 (tmm) cc_final: 0.8571 (tpt) REVERT: C 199 GLU cc_start: 0.9528 (tp30) cc_final: 0.9259 (tp30) REVERT: C 206 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7813 (ttpt) REVERT: C 208 LYS cc_start: 0.8738 (mtpp) cc_final: 0.8386 (mtpp) REVERT: C 216 ASP cc_start: 0.9118 (t70) cc_final: 0.8750 (t0) REVERT: C 250 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7779 (pp) REVERT: C 297 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8775 (tm) REVERT: C 311 LYS cc_start: 0.8705 (tmtt) cc_final: 0.8306 (tmtt) REVERT: C 337 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7251 (tt) REVERT: C 348 TYR cc_start: 0.9265 (t80) cc_final: 0.8994 (t80) REVERT: C 352 GLU cc_start: 0.8722 (tp30) cc_final: 0.8386 (tp30) REVERT: C 386 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8490 (pmm) REVERT: C 408 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8575 (mp) REVERT: C 420 MET cc_start: 0.7040 (mmm) cc_final: 0.6550 (mmm) REVERT: C 469 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.7874 (pt0) REVERT: C 470 ASP cc_start: 0.8595 (m-30) cc_final: 0.8349 (m-30) REVERT: C 488 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7818 (tp) REVERT: C 489 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8301 (tttt) REVERT: C 490 PHE cc_start: 0.8471 (m-80) cc_final: 0.8168 (m-80) REVERT: C 510 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6746 (mm-30) REVERT: D 32 TYR cc_start: 0.8492 (m-10) cc_final: 0.8256 (m-10) REVERT: D 73 VAL cc_start: 0.8235 (OUTLIER) cc_final: 0.7662 (t) REVERT: D 78 MET cc_start: 0.7617 (ttt) cc_final: 0.7192 (tmm) REVERT: D 165 PHE cc_start: 0.8006 (p90) cc_final: 0.7710 (p90) REVERT: D 199 GLU cc_start: 0.9492 (tp30) cc_final: 0.8878 (tp30) REVERT: D 202 GLN cc_start: 0.9340 (mm-40) cc_final: 0.9010 (mm-40) REVERT: D 203 ARG cc_start: 0.9388 (ptp-110) cc_final: 0.8728 (mtm-85) REVERT: D 216 ASP cc_start: 0.9036 (t70) cc_final: 0.8679 (t0) REVERT: D 265 GLN cc_start: 0.9275 (mm110) cc_final: 0.9066 (mm-40) REVERT: D 297 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8850 (tm) REVERT: D 311 LYS cc_start: 0.8714 (tmtt) cc_final: 0.7810 (tppt) REVERT: D 337 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7289 (tt) REVERT: D 355 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8354 (mtp85) REVERT: D 386 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8404 (ppp) REVERT: D 400 TYR cc_start: 0.7694 (m-80) cc_final: 0.7308 (m-80) REVERT: D 407 ARG cc_start: 0.7352 (ttt180) cc_final: 0.6775 (ttt180) REVERT: D 420 MET cc_start: 0.7138 (mmm) cc_final: 0.6741 (mmm) REVERT: D 470 ASP cc_start: 0.8809 (m-30) cc_final: 0.8338 (m-30) REVERT: D 488 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7583 (tp) REVERT: D 490 PHE cc_start: 0.8423 (m-80) cc_final: 0.8000 (m-80) REVERT: D 509 TYR cc_start: 0.7433 (p90) cc_final: 0.7028 (p90) REVERT: E 32 TYR cc_start: 0.8639 (m-10) cc_final: 0.8320 (m-10) REVERT: E 78 MET cc_start: 0.8108 (ttm) cc_final: 0.7713 (ttt) REVERT: E 109 LYS cc_start: 0.8860 (mmtm) cc_final: 0.8551 (mptt) REVERT: E 128 ARG cc_start: 0.8768 (mmt90) cc_final: 0.8486 (mmt90) REVERT: E 132 GLU cc_start: 0.9453 (mp0) cc_final: 0.9140 (mp0) REVERT: E 161 ARG cc_start: 0.9409 (mpp-170) cc_final: 0.9010 (mtm-85) REVERT: E 165 PHE cc_start: 0.8144 (p90) cc_final: 0.7882 (p90) REVERT: E 185 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7779 (mt) REVERT: E 206 LYS cc_start: 0.8031 (tppt) cc_final: 0.7652 (tppt) REVERT: E 216 ASP cc_start: 0.9161 (t70) cc_final: 0.8797 (t0) REVERT: E 250 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7874 (pp) REVERT: E 297 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8719 (tm) REVERT: E 311 LYS cc_start: 0.8772 (tmtt) cc_final: 0.8365 (tmtt) REVERT: E 337 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7318 (tt) REVERT: E 348 TYR cc_start: 0.9201 (t80) cc_final: 0.8949 (t80) REVERT: E 379 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9212 (tm) REVERT: E 386 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8400 (pmm) REVERT: E 400 TYR cc_start: 0.7529 (m-80) cc_final: 0.7259 (m-80) REVERT: E 407 ARG cc_start: 0.7427 (ttt180) cc_final: 0.6877 (tpt-90) REVERT: E 408 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8447 (mp) REVERT: E 420 MET cc_start: 0.7114 (mmm) cc_final: 0.6687 (mmm) REVERT: E 469 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.7794 (pt0) REVERT: E 470 ASP cc_start: 0.8665 (m-30) cc_final: 0.8319 (m-30) REVERT: E 482 MET cc_start: 0.8697 (tpt) cc_final: 0.8405 (tpt) REVERT: E 487 GLU cc_start: 0.8402 (pm20) cc_final: 0.7972 (pm20) REVERT: E 510 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6706 (mm-30) REVERT: F 32 TYR cc_start: 0.8466 (m-10) cc_final: 0.8090 (m-10) REVERT: F 62 LYS cc_start: 0.9253 (mmtp) cc_final: 0.8749 (mttm) REVERT: F 65 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9035 (pt) REVERT: F 78 MET cc_start: 0.8276 (ttm) cc_final: 0.7871 (ttt) REVERT: F 109 LYS cc_start: 0.8634 (mmtm) cc_final: 0.8252 (mptt) REVERT: F 132 GLU cc_start: 0.9486 (mp0) cc_final: 0.9219 (mp0) REVERT: F 161 ARG cc_start: 0.9403 (mpp-170) cc_final: 0.8854 (mtt90) REVERT: F 165 PHE cc_start: 0.8381 (p90) cc_final: 0.8033 (p90) REVERT: F 216 ASP cc_start: 0.9052 (t70) cc_final: 0.8707 (t0) REVERT: F 235 LEU cc_start: 0.9055 (mt) cc_final: 0.8463 (mt) REVERT: F 261 ASP cc_start: 0.8617 (OUTLIER) cc_final: 0.8342 (p0) REVERT: F 297 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8794 (tm) REVERT: F 311 LYS cc_start: 0.8786 (tmtt) cc_final: 0.7865 (tppt) REVERT: F 337 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7275 (tt) REVERT: F 386 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8482 (pmm) REVERT: F 466 HIS cc_start: 0.8587 (OUTLIER) cc_final: 0.7946 (t-90) REVERT: F 470 ASP cc_start: 0.8704 (m-30) cc_final: 0.8258 (m-30) REVERT: F 482 MET cc_start: 0.8689 (tpt) cc_final: 0.8435 (tpt) REVERT: F 490 PHE cc_start: 0.8520 (m-80) cc_final: 0.8253 (m-80) REVERT: F 509 TYR cc_start: 0.7407 (p90) cc_final: 0.6811 (p90) REVERT: F 510 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6506 (mm-30) REVERT: F 514 PHE cc_start: 0.7558 (p90) cc_final: 0.7074 (p90) REVERT: G 32 TYR cc_start: 0.8599 (m-80) cc_final: 0.8319 (m-10) REVERT: G 73 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.7416 (t) REVERT: G 74 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8423 (p) REVERT: G 109 LYS cc_start: 0.8842 (mmtm) cc_final: 0.8551 (mptt) REVERT: G 128 ARG cc_start: 0.8860 (mmt90) cc_final: 0.8462 (mmt90) REVERT: G 132 GLU cc_start: 0.9459 (mp0) cc_final: 0.9155 (mp0) REVERT: G 165 PHE cc_start: 0.8084 (p90) cc_final: 0.7683 (p90) REVERT: G 203 ARG cc_start: 0.9364 (ptp-110) cc_final: 0.9157 (ptp-110) REVERT: G 206 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7782 (ttpt) REVERT: G 216 ASP cc_start: 0.9140 (t70) cc_final: 0.8846 (t0) REVERT: G 297 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8762 (tm) REVERT: G 311 LYS cc_start: 0.8735 (tmtt) cc_final: 0.8356 (tmtt) REVERT: G 337 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7300 (tt) REVERT: G 379 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9189 (tm) REVERT: G 386 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8592 (pmm) REVERT: G 408 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8614 (mp) REVERT: G 420 MET cc_start: 0.6672 (mmm) cc_final: 0.6292 (mmm) REVERT: G 469 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.7942 (pt0) REVERT: G 470 ASP cc_start: 0.8769 (m-30) cc_final: 0.8447 (m-30) REVERT: G 482 MET cc_start: 0.8828 (tpt) cc_final: 0.8568 (tpt) REVERT: G 487 GLU cc_start: 0.8511 (pm20) cc_final: 0.8104 (pm20) REVERT: G 489 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7951 (tttt) REVERT: G 490 PHE cc_start: 0.8492 (m-80) cc_final: 0.8133 (m-80) REVERT: H 62 LYS cc_start: 0.9270 (mmtp) cc_final: 0.8741 (mttm) REVERT: H 66 VAL cc_start: 0.9112 (OUTLIER) cc_final: 0.8883 (p) REVERT: H 109 LYS cc_start: 0.8708 (mmtm) cc_final: 0.8425 (mptt) REVERT: H 165 PHE cc_start: 0.8106 (p90) cc_final: 0.7811 (p90) REVERT: H 199 GLU cc_start: 0.9489 (tp30) cc_final: 0.8865 (tp30) REVERT: H 202 GLN cc_start: 0.9343 (mm110) cc_final: 0.8966 (mm-40) REVERT: H 203 ARG cc_start: 0.9377 (ptp-110) cc_final: 0.9085 (ptp-110) REVERT: H 216 ASP cc_start: 0.9028 (t70) cc_final: 0.8678 (t0) REVERT: H 235 LEU cc_start: 0.9082 (mt) cc_final: 0.8430 (mt) REVERT: H 297 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8819 (tm) REVERT: H 311 LYS cc_start: 0.8714 (tmtt) cc_final: 0.7856 (tppt) REVERT: H 337 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7281 (tt) REVERT: H 386 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8530 (pmm) REVERT: H 469 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.7559 (pt0) REVERT: H 482 MET cc_start: 0.8755 (tpt) cc_final: 0.8478 (tpt) REVERT: H 487 GLU cc_start: 0.8414 (pm20) cc_final: 0.7984 (pm20) REVERT: H 488 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8105 (tm) REVERT: H 490 PHE cc_start: 0.8459 (m-80) cc_final: 0.8215 (m-80) outliers start: 281 outliers final: 176 residues processed: 1159 average time/residue: 0.1984 time to fit residues: 367.1311 Evaluate side-chains 1206 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 235 poor density : 971 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 489 LYS Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 294 TYR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 466 HIS Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 222 ILE Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 345 THR Chi-restraints excluded: chain H residue 355 ARG Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 469 GLN Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 494 THR Chi-restraints excluded: chain H residue 499 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 15 optimal weight: 9.9990 chunk 363 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 376 optimal weight: 7.9990 chunk 272 optimal weight: 0.0470 chunk 312 optimal weight: 6.9990 chunk 264 optimal weight: 7.9990 chunk 254 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 chunk 188 optimal weight: 0.8980 chunk 142 optimal weight: 6.9990 overall best weight: 2.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS B 303 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN D 303 ASN ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 HIS ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 GLN ** F 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN H 465 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.160324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.123605 restraints weight = 52089.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.128859 restraints weight = 30324.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.132576 restraints weight = 20849.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.135220 restraints weight = 15759.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.137188 restraints weight = 12724.052| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 31592 Z= 0.207 Angle : 0.845 12.544 42888 Z= 0.413 Chirality : 0.050 0.232 4888 Planarity : 0.005 0.070 5328 Dihedral : 15.883 141.097 5338 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 9.43 % Allowed : 28.98 % Favored : 61.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -2.28 (0.13), residues: 3880 helix: -1.61 (0.13), residues: 1304 sheet: -2.41 (0.21), residues: 512 loop : -1.09 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 355 TYR 0.039 0.002 TYR A 484 PHE 0.020 0.001 PHE F 90 HIS 0.007 0.001 HIS F 466 Details of bonding type rmsd covalent geometry : bond 0.00472 (31576) covalent geometry : angle 0.84543 (42888) hydrogen bonds : bond 0.03518 ( 832) hydrogen bonds : angle 5.40697 ( 2376) Misc. bond : bond 0.00031 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1314 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 301 poor density : 1013 time to evaluate : 1.159 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8027 (pp) REVERT: A 78 MET cc_start: 0.7363 (ttp) cc_final: 0.7154 (tmm) REVERT: A 109 LYS cc_start: 0.8916 (mmtm) cc_final: 0.8663 (mmtm) REVERT: A 128 ARG cc_start: 0.8848 (mmt90) cc_final: 0.8579 (mmt90) REVERT: A 165 PHE cc_start: 0.8066 (p90) cc_final: 0.7804 (p90) REVERT: A 203 ARG cc_start: 0.9153 (mpt180) cc_final: 0.8891 (mpt180) REVERT: A 216 ASP cc_start: 0.9008 (t70) cc_final: 0.8710 (t0) REVERT: A 297 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8782 (tm) REVERT: A 311 LYS cc_start: 0.8746 (tmtt) cc_final: 0.8301 (tmtt) REVERT: A 337 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7181 (tt) REVERT: A 352 GLU cc_start: 0.8688 (tp30) cc_final: 0.8356 (tp30) REVERT: A 379 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9142 (tm) REVERT: A 386 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8251 (ppp) REVERT: A 470 ASP cc_start: 0.8607 (m-30) cc_final: 0.8357 (m-30) REVERT: A 490 PHE cc_start: 0.8406 (m-80) cc_final: 0.8099 (m-80) REVERT: A 509 TYR cc_start: 0.7749 (p90) cc_final: 0.7542 (p90) REVERT: A 510 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6846 (mm-30) REVERT: B 109 LYS cc_start: 0.8792 (mmtm) cc_final: 0.8494 (mptt) REVERT: B 179 MET cc_start: 0.7575 (ptm) cc_final: 0.7340 (mtm) REVERT: B 202 GLN cc_start: 0.9364 (mm-40) cc_final: 0.9039 (mm-40) REVERT: B 216 ASP cc_start: 0.8985 (t70) cc_final: 0.8637 (t0) REVERT: B 250 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7781 (pp) REVERT: B 283 GLN cc_start: 0.8709 (tt0) cc_final: 0.8477 (mt0) REVERT: B 311 LYS cc_start: 0.8776 (tmtt) cc_final: 0.8344 (tmtt) REVERT: B 337 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7249 (tt) REVERT: B 352 GLU cc_start: 0.8830 (tp30) cc_final: 0.8623 (tp30) REVERT: B 355 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8555 (ttm110) REVERT: B 386 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8331 (pmm) REVERT: B 420 MET cc_start: 0.7369 (mmm) cc_final: 0.6936 (mmm) REVERT: B 470 ASP cc_start: 0.8677 (m-30) cc_final: 0.8379 (m-30) REVERT: B 482 MET cc_start: 0.8569 (tpt) cc_final: 0.8327 (tpt) REVERT: B 488 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7931 (tm) REVERT: B 490 PHE cc_start: 0.8477 (m-80) cc_final: 0.8159 (m-80) REVERT: C 32 TYR cc_start: 0.8602 (m-10) cc_final: 0.8391 (m-10) REVERT: C 62 LYS cc_start: 0.9169 (mmtp) cc_final: 0.8962 (mttm) REVERT: C 109 LYS cc_start: 0.8811 (mmtm) cc_final: 0.8520 (mptt) REVERT: C 166 LEU cc_start: 0.8145 (tp) cc_final: 0.7941 (tp) REVERT: C 179 MET cc_start: 0.7608 (ptm) cc_final: 0.7388 (ptm) REVERT: C 202 GLN cc_start: 0.9382 (mm-40) cc_final: 0.8853 (mm-40) REVERT: C 214 GLU cc_start: 0.9267 (mm-30) cc_final: 0.9028 (mp0) REVERT: C 250 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7856 (pp) REVERT: C 265 GLN cc_start: 0.9244 (mm110) cc_final: 0.8967 (mm-40) REVERT: C 297 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8810 (tm) REVERT: C 311 LYS cc_start: 0.8721 (tmtt) cc_final: 0.8285 (tmtt) REVERT: C 337 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7220 (tt) REVERT: C 352 GLU cc_start: 0.8678 (tp30) cc_final: 0.8388 (tp30) REVERT: C 386 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8319 (ppp) REVERT: C 420 MET cc_start: 0.7259 (mmm) cc_final: 0.6739 (mmm) REVERT: C 469 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.7848 (pt0) REVERT: C 470 ASP cc_start: 0.8596 (m-30) cc_final: 0.8315 (m-30) REVERT: C 488 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7898 (tp) REVERT: C 489 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8294 (tttt) REVERT: C 490 PHE cc_start: 0.8368 (m-80) cc_final: 0.8085 (m-80) REVERT: C 509 TYR cc_start: 0.7485 (p90) cc_final: 0.7061 (p90) REVERT: C 510 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6679 (mm-30) REVERT: C 514 PHE cc_start: 0.7467 (p90) cc_final: 0.6968 (p90) REVERT: D 32 TYR cc_start: 0.8597 (m-10) cc_final: 0.8351 (m-10) REVERT: D 73 VAL cc_start: 0.8416 (OUTLIER) cc_final: 0.6901 (t) REVERT: D 78 MET cc_start: 0.7842 (ttt) cc_final: 0.7449 (ttt) REVERT: D 165 PHE cc_start: 0.8024 (p90) cc_final: 0.7740 (p90) REVERT: D 199 GLU cc_start: 0.9473 (tp30) cc_final: 0.8837 (tp30) REVERT: D 202 GLN cc_start: 0.9371 (mm-40) cc_final: 0.9010 (mm-40) REVERT: D 203 ARG cc_start: 0.9345 (ptp-110) cc_final: 0.9042 (ptp-110) REVERT: D 216 ASP cc_start: 0.8987 (t70) cc_final: 0.8648 (t0) REVERT: D 265 GLN cc_start: 0.9262 (mm110) cc_final: 0.9026 (mm-40) REVERT: D 297 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8852 (tm) REVERT: D 311 LYS cc_start: 0.8706 (tmtt) cc_final: 0.8267 (tmtt) REVERT: D 337 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7336 (tt) REVERT: D 355 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8366 (mtp85) REVERT: D 386 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8021 (pmm) REVERT: D 420 MET cc_start: 0.7349 (mmm) cc_final: 0.6915 (mmm) REVERT: D 469 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.7758 (pt0) REVERT: D 470 ASP cc_start: 0.8711 (m-30) cc_final: 0.8367 (m-30) REVERT: D 488 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7682 (tp) REVERT: D 490 PHE cc_start: 0.8394 (m-80) cc_final: 0.7958 (m-80) REVERT: E 32 TYR cc_start: 0.8599 (m-10) cc_final: 0.8365 (m-10) REVERT: E 78 MET cc_start: 0.8172 (ttm) cc_final: 0.7835 (ttt) REVERT: E 109 LYS cc_start: 0.8827 (mmtm) cc_final: 0.8542 (mptt) REVERT: E 128 ARG cc_start: 0.8761 (mmt90) cc_final: 0.8422 (mmt90) REVERT: E 132 GLU cc_start: 0.9466 (mp0) cc_final: 0.9089 (mp0) REVERT: E 165 PHE cc_start: 0.8117 (p90) cc_final: 0.7828 (p90) REVERT: E 166 LEU cc_start: 0.7984 (tp) cc_final: 0.7714 (tp) REVERT: E 179 MET cc_start: 0.7561 (ptm) cc_final: 0.7330 (mtm) REVERT: E 185 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7875 (mt) REVERT: E 206 LYS cc_start: 0.8170 (tppt) cc_final: 0.7830 (tppt) REVERT: E 216 ASP cc_start: 0.9126 (t70) cc_final: 0.8772 (t0) REVERT: E 250 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7866 (pp) REVERT: E 297 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8750 (tm) REVERT: E 311 LYS cc_start: 0.8791 (tmtt) cc_final: 0.8367 (tmtt) REVERT: E 337 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7146 (tt) REVERT: E 379 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9188 (tm) REVERT: E 386 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8546 (pmm) REVERT: E 408 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8489 (mp) REVERT: E 420 MET cc_start: 0.7351 (mmm) cc_final: 0.6892 (mmm) REVERT: E 469 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.7812 (pt0) REVERT: E 470 ASP cc_start: 0.8661 (m-30) cc_final: 0.8327 (m-30) REVERT: E 509 TYR cc_start: 0.7506 (p90) cc_final: 0.6995 (p90) REVERT: E 510 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6648 (mm-30) REVERT: F 32 TYR cc_start: 0.8571 (m-10) cc_final: 0.8257 (m-10) REVERT: F 62 LYS cc_start: 0.9279 (mmtp) cc_final: 0.8753 (mttm) REVERT: F 65 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9070 (pt) REVERT: F 78 MET cc_start: 0.8274 (ttm) cc_final: 0.7663 (ttp) REVERT: F 109 LYS cc_start: 0.8690 (mmtm) cc_final: 0.8327 (mptt) REVERT: F 128 ARG cc_start: 0.8915 (mmt90) cc_final: 0.8690 (mmt90) REVERT: F 132 GLU cc_start: 0.9490 (mp0) cc_final: 0.9193 (mp0) REVERT: F 165 PHE cc_start: 0.8408 (p90) cc_final: 0.7988 (p90) REVERT: F 216 ASP cc_start: 0.8983 (t70) cc_final: 0.8649 (t0) REVERT: F 235 LEU cc_start: 0.9035 (mt) cc_final: 0.8457 (mt) REVERT: F 261 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8249 (p0) REVERT: F 283 GLN cc_start: 0.8596 (tt0) cc_final: 0.8374 (mt0) REVERT: F 297 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8842 (tm) REVERT: F 311 LYS cc_start: 0.8784 (tmtt) cc_final: 0.8344 (tmtt) REVERT: F 337 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7301 (tt) REVERT: F 386 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8470 (pmm) REVERT: F 408 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8676 (mp) REVERT: F 466 HIS cc_start: 0.8577 (OUTLIER) cc_final: 0.7647 (t-90) REVERT: F 469 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.7749 (pt0) REVERT: F 470 ASP cc_start: 0.8694 (m-30) cc_final: 0.8328 (m-30) REVERT: F 482 MET cc_start: 0.8675 (tpt) cc_final: 0.8435 (tpt) REVERT: F 488 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7659 (tp) REVERT: F 490 PHE cc_start: 0.8503 (m-80) cc_final: 0.8282 (m-80) REVERT: F 510 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6570 (mm-30) REVERT: F 514 PHE cc_start: 0.7636 (p90) cc_final: 0.7031 (p90) REVERT: G 32 TYR cc_start: 0.8590 (m-10) cc_final: 0.8228 (m-10) REVERT: G 109 LYS cc_start: 0.8865 (mmtm) cc_final: 0.8634 (mptt) REVERT: G 128 ARG cc_start: 0.8805 (mmt90) cc_final: 0.8479 (mmt90) REVERT: G 132 GLU cc_start: 0.9457 (mp0) cc_final: 0.9077 (mp0) REVERT: G 165 PHE cc_start: 0.8038 (p90) cc_final: 0.7643 (p90) REVERT: G 199 GLU cc_start: 0.9516 (tp30) cc_final: 0.9277 (tp30) REVERT: G 203 ARG cc_start: 0.9367 (ptp-110) cc_final: 0.9096 (ptp-110) REVERT: G 216 ASP cc_start: 0.9103 (t70) cc_final: 0.8796 (t0) REVERT: G 297 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8801 (tm) REVERT: G 311 LYS cc_start: 0.8789 (tmtt) cc_final: 0.8380 (tmtt) REVERT: G 337 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7290 (tt) REVERT: G 379 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9168 (tm) REVERT: G 386 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8564 (pmm) REVERT: G 407 ARG cc_start: 0.7543 (ttt180) cc_final: 0.7214 (ttt90) REVERT: G 408 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8483 (mp) REVERT: G 420 MET cc_start: 0.7087 (mmm) cc_final: 0.6657 (mmm) REVERT: G 469 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.7872 (pt0) REVERT: G 470 ASP cc_start: 0.8691 (m-30) cc_final: 0.8390 (m-30) REVERT: G 489 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8019 (tttt) REVERT: G 490 PHE cc_start: 0.8425 (m-80) cc_final: 0.8072 (m-80) REVERT: G 509 TYR cc_start: 0.7571 (p90) cc_final: 0.7269 (p90) REVERT: H 62 LYS cc_start: 0.9286 (mmtp) cc_final: 0.8751 (mttm) REVERT: H 66 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8683 (p) REVERT: H 78 MET cc_start: 0.7701 (ttt) cc_final: 0.7429 (tmm) REVERT: H 109 LYS cc_start: 0.8745 (mmtm) cc_final: 0.8490 (mptt) REVERT: H 128 ARG cc_start: 0.8772 (mmt90) cc_final: 0.8397 (mmt90) REVERT: H 161 ARG cc_start: 0.9407 (mpp-170) cc_final: 0.8916 (mtt90) REVERT: H 165 PHE cc_start: 0.8077 (p90) cc_final: 0.7656 (p90) REVERT: H 179 MET cc_start: 0.7440 (ptm) cc_final: 0.7208 (ptm) REVERT: H 199 GLU cc_start: 0.9497 (tp30) cc_final: 0.8814 (tp30) REVERT: H 202 GLN cc_start: 0.9335 (mm110) cc_final: 0.8968 (mm110) REVERT: H 203 ARG cc_start: 0.9346 (ptp-110) cc_final: 0.9042 (ptp-110) REVERT: H 206 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7724 (ttpt) REVERT: H 208 LYS cc_start: 0.8476 (ttmm) cc_final: 0.7631 (mtmt) REVERT: H 216 ASP cc_start: 0.8981 (t70) cc_final: 0.8643 (t0) REVERT: H 235 LEU cc_start: 0.9065 (mt) cc_final: 0.8441 (mt) REVERT: H 250 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8006 (pp) REVERT: H 283 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8327 (mt0) REVERT: H 297 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8819 (tm) REVERT: H 311 LYS cc_start: 0.8749 (tmtt) cc_final: 0.8339 (tmtt) REVERT: H 337 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7204 (tt) REVERT: H 352 GLU cc_start: 0.8849 (tp30) cc_final: 0.8227 (tp30) REVERT: H 386 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8553 (pmm) REVERT: H 469 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.7577 (pt0) REVERT: H 470 ASP cc_start: 0.8751 (m-30) cc_final: 0.8379 (m-30) REVERT: H 488 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7921 (tp) REVERT: H 490 PHE cc_start: 0.8489 (m-80) cc_final: 0.8248 (m-80) REVERT: H 509 TYR cc_start: 0.7632 (p90) cc_final: 0.7254 (p90) outliers start: 301 outliers final: 196 residues processed: 1147 average time/residue: 0.1969 time to fit residues: 362.9065 Evaluate side-chains 1204 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 257 poor density : 947 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 489 LYS Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 294 TYR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 355 ARG Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 466 HIS Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 222 ILE Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain H residue 469 GLN Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 494 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 221 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 112 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 181 optimal weight: 1.9990 chunk 310 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 316 optimal weight: 3.9990 chunk 311 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS D 283 GLN ** D 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 253 HIS ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 253 HIS ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.168150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.129763 restraints weight = 51975.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.135442 restraints weight = 29696.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.139439 restraints weight = 20193.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.142304 restraints weight = 15176.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.144331 restraints weight = 12200.162| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31592 Z= 0.189 Angle : 0.868 11.293 42888 Z= 0.421 Chirality : 0.051 0.246 4888 Planarity : 0.005 0.090 5328 Dihedral : 15.696 140.505 5334 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 9.12 % Allowed : 30.36 % Favored : 60.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -2.36 (0.13), residues: 3880 helix: -1.61 (0.13), residues: 1296 sheet: -2.48 (0.20), residues: 528 loop : -1.16 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG H 355 TYR 0.031 0.002 TYR D 509 PHE 0.019 0.001 PHE B 90 HIS 0.009 0.001 HIS G 466 Details of bonding type rmsd covalent geometry : bond 0.00439 (31576) covalent geometry : angle 0.86779 (42888) hydrogen bonds : bond 0.03535 ( 832) hydrogen bonds : angle 5.45492 ( 2376) Misc. bond : bond 0.00027 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1314 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 291 poor density : 1023 time to evaluate : 1.144 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8609 (m-10) cc_final: 0.8307 (m-10) REVERT: A 51 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8032 (pp) REVERT: A 109 LYS cc_start: 0.8860 (mmtm) cc_final: 0.8589 (mppt) REVERT: A 128 ARG cc_start: 0.8863 (mmt90) cc_final: 0.8614 (mmt90) REVERT: A 165 PHE cc_start: 0.8092 (p90) cc_final: 0.7792 (p90) REVERT: A 202 GLN cc_start: 0.9380 (mt0) cc_final: 0.8985 (mt0) REVERT: A 216 ASP cc_start: 0.9036 (t70) cc_final: 0.8732 (t0) REVERT: A 250 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8085 (pp) REVERT: A 297 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8793 (tm) REVERT: A 311 LYS cc_start: 0.8655 (tmtt) cc_final: 0.8204 (tmtt) REVERT: A 337 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7170 (tt) REVERT: A 352 GLU cc_start: 0.8654 (tp30) cc_final: 0.8311 (tp30) REVERT: A 379 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9188 (tm) REVERT: A 385 MET cc_start: 0.7382 (ttt) cc_final: 0.6328 (mmm) REVERT: A 386 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8211 (ppp) REVERT: A 469 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.7863 (pt0) REVERT: A 470 ASP cc_start: 0.8597 (m-30) cc_final: 0.8315 (m-30) REVERT: A 490 PHE cc_start: 0.8457 (m-80) cc_final: 0.8056 (m-80) REVERT: A 510 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6796 (mm-30) REVERT: B 32 TYR cc_start: 0.8539 (m-10) cc_final: 0.8221 (m-10) REVERT: B 109 LYS cc_start: 0.8783 (mmtm) cc_final: 0.8433 (mptt) REVERT: B 111 GLU cc_start: 0.8811 (mp0) cc_final: 0.8604 (mp0) REVERT: B 128 ARG cc_start: 0.9040 (mmm-85) cc_final: 0.8749 (mmt90) REVERT: B 166 LEU cc_start: 0.8086 (tp) cc_final: 0.7856 (tp) REVERT: B 202 GLN cc_start: 0.9376 (mm-40) cc_final: 0.9088 (mm-40) REVERT: B 203 ARG cc_start: 0.9242 (ptp-110) cc_final: 0.9034 (ptp-110) REVERT: B 216 ASP cc_start: 0.9026 (t70) cc_final: 0.8657 (t0) REVERT: B 261 ASP cc_start: 0.8654 (p0) cc_final: 0.8322 (p0) REVERT: B 283 GLN cc_start: 0.8777 (tt0) cc_final: 0.8518 (mt0) REVERT: B 311 LYS cc_start: 0.8730 (tmtt) cc_final: 0.8279 (tmtt) REVERT: B 337 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7238 (tt) REVERT: B 352 GLU cc_start: 0.8798 (tp30) cc_final: 0.8553 (tp30) REVERT: B 386 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8278 (pmm) REVERT: B 420 MET cc_start: 0.7357 (mmm) cc_final: 0.6967 (mmm) REVERT: B 469 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.7866 (pt0) REVERT: B 470 ASP cc_start: 0.8793 (m-30) cc_final: 0.8284 (m-30) REVERT: B 482 MET cc_start: 0.8693 (tpt) cc_final: 0.8415 (tpt) REVERT: B 490 PHE cc_start: 0.8497 (m-80) cc_final: 0.8170 (m-80) REVERT: C 32 TYR cc_start: 0.8648 (m-10) cc_final: 0.8402 (m-10) REVERT: C 62 LYS cc_start: 0.9079 (mmtp) cc_final: 0.8672 (mtmt) REVERT: C 109 LYS cc_start: 0.8730 (mmtm) cc_final: 0.8458 (mptt) REVERT: C 128 ARG cc_start: 0.8786 (mmt90) cc_final: 0.8558 (mmt180) REVERT: C 132 GLU cc_start: 0.9436 (mp0) cc_final: 0.9107 (mp0) REVERT: C 150 MET cc_start: 0.8989 (tmm) cc_final: 0.8513 (tpt) REVERT: C 166 LEU cc_start: 0.8141 (tp) cc_final: 0.7918 (tp) REVERT: C 179 MET cc_start: 0.7673 (ptm) cc_final: 0.7458 (ptm) REVERT: C 202 GLN cc_start: 0.9396 (mm-40) cc_final: 0.8885 (mm-40) REVERT: C 216 ASP cc_start: 0.9128 (t70) cc_final: 0.8763 (t0) REVERT: C 250 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7797 (pp) REVERT: C 265 GLN cc_start: 0.9288 (mm110) cc_final: 0.9073 (mm-40) REVERT: C 297 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8822 (tm) REVERT: C 311 LYS cc_start: 0.8627 (tmtt) cc_final: 0.8264 (ttpp) REVERT: C 337 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7042 (tt) REVERT: C 348 TYR cc_start: 0.9266 (t80) cc_final: 0.8942 (t80) REVERT: C 352 GLU cc_start: 0.8727 (tp30) cc_final: 0.8360 (tp30) REVERT: C 386 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8316 (ppp) REVERT: C 420 MET cc_start: 0.7411 (mmm) cc_final: 0.6825 (mmm) REVERT: C 469 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.7854 (pt0) REVERT: C 470 ASP cc_start: 0.8609 (m-30) cc_final: 0.8267 (m-30) REVERT: C 488 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7896 (tp) REVERT: C 490 PHE cc_start: 0.8334 (m-80) cc_final: 0.8047 (m-80) REVERT: C 510 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6755 (mm-30) REVERT: D 109 LYS cc_start: 0.8566 (mmtm) cc_final: 0.8205 (mmmm) REVERT: D 128 ARG cc_start: 0.8870 (mmt90) cc_final: 0.8416 (mmt90) REVERT: D 165 PHE cc_start: 0.8052 (p90) cc_final: 0.7721 (p90) REVERT: D 166 LEU cc_start: 0.8192 (tp) cc_final: 0.7913 (tp) REVERT: D 199 GLU cc_start: 0.9496 (tp30) cc_final: 0.8902 (tp30) REVERT: D 202 GLN cc_start: 0.9393 (mm-40) cc_final: 0.9121 (mm-40) REVERT: D 203 ARG cc_start: 0.9360 (ptp-110) cc_final: 0.9066 (ptp-110) REVERT: D 216 ASP cc_start: 0.9045 (t70) cc_final: 0.8671 (t0) REVERT: D 261 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8366 (p0) REVERT: D 265 GLN cc_start: 0.9302 (mm110) cc_final: 0.9065 (mm-40) REVERT: D 297 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8895 (tm) REVERT: D 311 LYS cc_start: 0.8650 (tmtt) cc_final: 0.8233 (tmtt) REVERT: D 337 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7279 (tt) REVERT: D 386 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8056 (pmm) REVERT: D 395 GLU cc_start: 0.8418 (pm20) cc_final: 0.8190 (pm20) REVERT: D 420 MET cc_start: 0.7247 (mmm) cc_final: 0.6834 (mmm) REVERT: D 469 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.7666 (pt0) REVERT: D 470 ASP cc_start: 0.8754 (m-30) cc_final: 0.8378 (m-30) REVERT: D 488 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7563 (tp) REVERT: D 490 PHE cc_start: 0.8425 (m-80) cc_final: 0.7905 (m-80) REVERT: E 32 TYR cc_start: 0.8625 (m-10) cc_final: 0.8314 (m-10) REVERT: E 66 VAL cc_start: 0.8864 (OUTLIER) cc_final: 0.8457 (p) REVERT: E 78 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7791 (ttt) REVERT: E 109 LYS cc_start: 0.8741 (mmtm) cc_final: 0.8492 (mptt) REVERT: E 128 ARG cc_start: 0.8767 (mmt90) cc_final: 0.8292 (mmt90) REVERT: E 165 PHE cc_start: 0.8134 (p90) cc_final: 0.7802 (p90) REVERT: E 166 LEU cc_start: 0.8133 (tp) cc_final: 0.7818 (tp) REVERT: E 185 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7872 (mt) REVERT: E 206 LYS cc_start: 0.8155 (tppt) cc_final: 0.7829 (tppt) REVERT: E 216 ASP cc_start: 0.9162 (t70) cc_final: 0.8791 (t0) REVERT: E 250 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7863 (pp) REVERT: E 283 GLN cc_start: 0.8774 (tt0) cc_final: 0.8546 (mt0) REVERT: E 297 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8775 (tm) REVERT: E 311 LYS cc_start: 0.8714 (tmtt) cc_final: 0.8292 (tmtt) REVERT: E 337 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7109 (tt) REVERT: E 379 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9210 (tm) REVERT: E 386 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8478 (pmm) REVERT: E 390 LEU cc_start: 0.8936 (tt) cc_final: 0.8544 (tt) REVERT: E 407 ARG cc_start: 0.7402 (ttt180) cc_final: 0.6857 (ttt-90) REVERT: E 408 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8521 (mp) REVERT: E 420 MET cc_start: 0.7410 (mmm) cc_final: 0.6962 (mmm) REVERT: E 469 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.7764 (pt0) REVERT: E 470 ASP cc_start: 0.8662 (m-30) cc_final: 0.8300 (m-30) REVERT: E 509 TYR cc_start: 0.7529 (p90) cc_final: 0.7130 (p90) REVERT: E 510 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6684 (mm-30) REVERT: F 32 TYR cc_start: 0.8656 (m-10) cc_final: 0.8390 (m-10) REVERT: F 62 LYS cc_start: 0.9285 (mmtp) cc_final: 0.9005 (mttm) REVERT: F 65 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9025 (pt) REVERT: F 66 VAL cc_start: 0.8714 (OUTLIER) cc_final: 0.8291 (p) REVERT: F 78 MET cc_start: 0.8235 (ttm) cc_final: 0.7553 (ttp) REVERT: F 109 LYS cc_start: 0.8675 (mmtm) cc_final: 0.8379 (mptt) REVERT: F 128 ARG cc_start: 0.8917 (mmt90) cc_final: 0.8673 (mmt90) REVERT: F 132 GLU cc_start: 0.9482 (mp0) cc_final: 0.9175 (mp0) REVERT: F 161 ARG cc_start: 0.9419 (mpp-170) cc_final: 0.8965 (mtt90) REVERT: F 165 PHE cc_start: 0.8488 (p90) cc_final: 0.7902 (p90) REVERT: F 166 LEU cc_start: 0.8117 (tp) cc_final: 0.7814 (tp) REVERT: F 206 LYS cc_start: 0.8148 (mtmt) cc_final: 0.7668 (ttpt) REVERT: F 216 ASP cc_start: 0.9003 (t70) cc_final: 0.8713 (t0) REVERT: F 261 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8415 (p0) REVERT: F 283 GLN cc_start: 0.8725 (tt0) cc_final: 0.8491 (mt0) REVERT: F 297 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8843 (tm) REVERT: F 311 LYS cc_start: 0.8751 (tmtt) cc_final: 0.8326 (tmtt) REVERT: F 337 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7255 (tt) REVERT: F 386 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8472 (pmm) REVERT: F 466 HIS cc_start: 0.8532 (OUTLIER) cc_final: 0.7622 (t-90) REVERT: F 469 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.7848 (pt0) REVERT: F 470 ASP cc_start: 0.8712 (m-30) cc_final: 0.8215 (m-30) REVERT: F 482 MET cc_start: 0.8770 (tpt) cc_final: 0.8543 (tpt) REVERT: F 488 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7654 (tp) REVERT: F 490 PHE cc_start: 0.8535 (m-80) cc_final: 0.8263 (m-80) REVERT: F 510 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6542 (mm-30) REVERT: G 32 TYR cc_start: 0.8618 (m-10) cc_final: 0.8255 (m-10) REVERT: G 55 LEU cc_start: 0.9057 (tt) cc_final: 0.8775 (tp) REVERT: G 109 LYS cc_start: 0.8837 (mmtm) cc_final: 0.8594 (mptt) REVERT: G 165 PHE cc_start: 0.8105 (p90) cc_final: 0.7818 (p90) REVERT: G 166 LEU cc_start: 0.8153 (tp) cc_final: 0.7856 (tp) REVERT: G 199 GLU cc_start: 0.9549 (tp30) cc_final: 0.9300 (tp30) REVERT: G 203 ARG cc_start: 0.9380 (ptp-110) cc_final: 0.9105 (ptp-110) REVERT: G 216 ASP cc_start: 0.9145 (t70) cc_final: 0.8826 (t0) REVERT: G 297 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8799 (tm) REVERT: G 311 LYS cc_start: 0.8652 (tmtt) cc_final: 0.8207 (tmtt) REVERT: G 337 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7145 (tt) REVERT: G 352 GLU cc_start: 0.8720 (tp30) cc_final: 0.8408 (tp30) REVERT: G 379 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9200 (tm) REVERT: G 386 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8468 (pmm) REVERT: G 407 ARG cc_start: 0.7558 (ttt180) cc_final: 0.7264 (ttt90) REVERT: G 408 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8536 (mp) REVERT: G 420 MET cc_start: 0.7098 (mmm) cc_final: 0.6691 (mmm) REVERT: G 469 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.7802 (pt0) REVERT: G 470 ASP cc_start: 0.8756 (m-30) cc_final: 0.8427 (m-30) REVERT: G 489 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7998 (tttt) REVERT: G 490 PHE cc_start: 0.8431 (m-80) cc_final: 0.7993 (m-80) REVERT: G 509 TYR cc_start: 0.7636 (p90) cc_final: 0.7213 (p90) REVERT: H 62 LYS cc_start: 0.9300 (mmtp) cc_final: 0.9019 (mttm) REVERT: H 66 VAL cc_start: 0.8844 (OUTLIER) cc_final: 0.8335 (p) REVERT: H 78 MET cc_start: 0.7594 (ttt) cc_final: 0.7329 (tmm) REVERT: H 109 LYS cc_start: 0.8703 (mmtm) cc_final: 0.8450 (mptt) REVERT: H 128 ARG cc_start: 0.8795 (mmt90) cc_final: 0.8281 (mmt90) REVERT: H 165 PHE cc_start: 0.8077 (p90) cc_final: 0.7618 (p90) REVERT: H 199 GLU cc_start: 0.9513 (tp30) cc_final: 0.8876 (tp30) REVERT: H 202 GLN cc_start: 0.9372 (mm110) cc_final: 0.9042 (mm110) REVERT: H 203 ARG cc_start: 0.9330 (ptp-110) cc_final: 0.9001 (ptp-110) REVERT: H 206 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7672 (ttpt) REVERT: H 208 LYS cc_start: 0.8460 (ttmm) cc_final: 0.7620 (mtmt) REVERT: H 216 ASP cc_start: 0.9019 (t70) cc_final: 0.8668 (t0) REVERT: H 250 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.7978 (pp) REVERT: H 297 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8816 (tm) REVERT: H 311 LYS cc_start: 0.8679 (tmtt) cc_final: 0.8234 (tmtt) REVERT: H 337 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7176 (tt) REVERT: H 386 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8382 (pmm) REVERT: H 469 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.7419 (pt0) REVERT: H 470 ASP cc_start: 0.8750 (m-30) cc_final: 0.8344 (m-30) REVERT: H 488 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7917 (tp) REVERT: H 490 PHE cc_start: 0.8536 (m-80) cc_final: 0.8223 (m-80) REVERT: H 509 TYR cc_start: 0.7619 (p90) cc_final: 0.7370 (p90) outliers start: 291 outliers final: 194 residues processed: 1148 average time/residue: 0.1913 time to fit residues: 352.0751 Evaluate side-chains 1234 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 254 poor density : 980 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 294 TYR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 355 ARG Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 466 HIS Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 222 ILE Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 345 THR Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain H residue 469 GLN Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 494 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 203 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 255 optimal weight: 7.9990 chunk 277 optimal weight: 4.9990 chunk 243 optimal weight: 0.7980 chunk 347 optimal weight: 9.9990 chunk 307 optimal weight: 1.9990 chunk 226 optimal weight: 0.7980 chunk 278 optimal weight: 0.9990 chunk 311 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN B 469 GLN ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN D 283 GLN ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 GLN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 465 GLN F 469 GLN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 298 GLN G 465 GLN ** G 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN H 469 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.173753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.136792 restraints weight = 51129.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.142684 restraints weight = 28811.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.146787 restraints weight = 19271.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.149659 restraints weight = 14258.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.151833 restraints weight = 11314.942| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 31592 Z= 0.150 Angle : 0.879 13.877 42888 Z= 0.421 Chirality : 0.050 0.230 4888 Planarity : 0.005 0.090 5328 Dihedral : 15.545 140.474 5334 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 7.27 % Allowed : 32.42 % Favored : 60.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -2.20 (0.13), residues: 3880 helix: -1.36 (0.13), residues: 1240 sheet: -2.50 (0.20), residues: 528 loop : -1.14 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 355 TYR 0.031 0.002 TYR D 509 PHE 0.012 0.001 PHE B 165 HIS 0.007 0.001 HIS H 466 Details of bonding type rmsd covalent geometry : bond 0.00349 (31576) covalent geometry : angle 0.87892 (42888) hydrogen bonds : bond 0.03439 ( 832) hydrogen bonds : angle 5.34075 ( 2376) Misc. bond : bond 0.00034 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1294 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 1062 time to evaluate : 1.145 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8571 (m-10) cc_final: 0.8312 (m-10) REVERT: A 51 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8042 (pp) REVERT: A 74 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.7529 (p) REVERT: A 111 GLU cc_start: 0.8776 (mp0) cc_final: 0.8262 (pm20) REVERT: A 165 PHE cc_start: 0.8048 (p90) cc_final: 0.7749 (p90) REVERT: A 202 GLN cc_start: 0.9359 (mt0) cc_final: 0.8219 (mt0) REVERT: A 216 ASP cc_start: 0.9002 (t70) cc_final: 0.8711 (t0) REVERT: A 250 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8102 (pp) REVERT: A 311 LYS cc_start: 0.8655 (tmtt) cc_final: 0.8183 (tmtt) REVERT: A 337 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7100 (tt) REVERT: A 352 GLU cc_start: 0.8641 (tp30) cc_final: 0.8318 (tp30) REVERT: A 385 MET cc_start: 0.7015 (ttt) cc_final: 0.6404 (mmm) REVERT: A 386 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8089 (ppp) REVERT: A 469 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.7878 (pt0) REVERT: A 470 ASP cc_start: 0.8629 (m-30) cc_final: 0.8349 (m-30) REVERT: A 490 PHE cc_start: 0.8371 (m-80) cc_final: 0.8051 (m-80) REVERT: A 509 TYR cc_start: 0.7396 (p90) cc_final: 0.7001 (p90) REVERT: A 510 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.7048 (mm-30) REVERT: B 32 TYR cc_start: 0.8584 (m-10) cc_final: 0.8286 (m-10) REVERT: B 109 LYS cc_start: 0.8744 (mmtm) cc_final: 0.8442 (mptt) REVERT: B 166 LEU cc_start: 0.8161 (tp) cc_final: 0.7923 (tp) REVERT: B 202 GLN cc_start: 0.9361 (mm-40) cc_final: 0.9068 (mm-40) REVERT: B 216 ASP cc_start: 0.8959 (t70) cc_final: 0.8608 (t0) REVERT: B 261 ASP cc_start: 0.8619 (p0) cc_final: 0.8289 (p0) REVERT: B 283 GLN cc_start: 0.8589 (tt0) cc_final: 0.8354 (mt0) REVERT: B 311 LYS cc_start: 0.8698 (tmtt) cc_final: 0.8238 (tmtt) REVERT: B 337 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7134 (tt) REVERT: B 386 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8230 (pmm) REVERT: B 420 MET cc_start: 0.7422 (mmm) cc_final: 0.6663 (mmt) REVERT: B 469 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.7840 (pt0) REVERT: B 470 ASP cc_start: 0.8764 (m-30) cc_final: 0.8299 (m-30) REVERT: B 482 MET cc_start: 0.8641 (tpt) cc_final: 0.8363 (tpt) REVERT: B 490 PHE cc_start: 0.8421 (m-80) cc_final: 0.8105 (m-80) REVERT: C 62 LYS cc_start: 0.9031 (mmtp) cc_final: 0.8535 (mtmt) REVERT: C 109 LYS cc_start: 0.8589 (mmtm) cc_final: 0.8372 (mptt) REVERT: C 128 ARG cc_start: 0.8765 (mmt90) cc_final: 0.8485 (mmt180) REVERT: C 132 GLU cc_start: 0.9426 (mp0) cc_final: 0.9079 (mp0) REVERT: C 150 MET cc_start: 0.8954 (tmm) cc_final: 0.8500 (tpt) REVERT: C 166 LEU cc_start: 0.8154 (tp) cc_final: 0.7938 (tp) REVERT: C 179 MET cc_start: 0.7618 (ptm) cc_final: 0.7381 (ptm) REVERT: C 214 GLU cc_start: 0.9289 (mm-30) cc_final: 0.9029 (mp0) REVERT: C 216 ASP cc_start: 0.9076 (t70) cc_final: 0.8723 (t0) REVERT: C 250 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7822 (pp) REVERT: C 262 LEU cc_start: 0.9359 (tp) cc_final: 0.9151 (tp) REVERT: C 265 GLN cc_start: 0.9255 (mm110) cc_final: 0.9013 (mm-40) REVERT: C 297 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8767 (tm) REVERT: C 311 LYS cc_start: 0.8611 (tmtt) cc_final: 0.8250 (ttpp) REVERT: C 337 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.6928 (tt) REVERT: C 348 TYR cc_start: 0.9188 (t80) cc_final: 0.8961 (t80) REVERT: C 352 GLU cc_start: 0.8750 (tp30) cc_final: 0.8425 (tp30) REVERT: C 420 MET cc_start: 0.7352 (mmm) cc_final: 0.6847 (mmm) REVERT: C 450 LYS cc_start: 0.8907 (mtmm) cc_final: 0.8317 (mtmm) REVERT: C 469 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.7715 (pt0) REVERT: C 490 PHE cc_start: 0.8298 (m-80) cc_final: 0.7918 (m-80) REVERT: C 510 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.7002 (mm-30) REVERT: D 32 TYR cc_start: 0.8574 (m-10) cc_final: 0.8102 (m-10) REVERT: D 109 LYS cc_start: 0.8554 (mmtm) cc_final: 0.8190 (mmmm) REVERT: D 128 ARG cc_start: 0.8889 (mmt90) cc_final: 0.8511 (mmt90) REVERT: D 161 ARG cc_start: 0.9356 (mpp-170) cc_final: 0.9060 (mtt90) REVERT: D 165 PHE cc_start: 0.7999 (p90) cc_final: 0.7690 (p90) REVERT: D 166 LEU cc_start: 0.8306 (tp) cc_final: 0.8016 (tp) REVERT: D 199 GLU cc_start: 0.9457 (tp30) cc_final: 0.9094 (tp30) REVERT: D 202 GLN cc_start: 0.9371 (mm-40) cc_final: 0.8941 (mm-40) REVERT: D 203 ARG cc_start: 0.9318 (ptp-110) cc_final: 0.9098 (ptp-110) REVERT: D 216 ASP cc_start: 0.8983 (t70) cc_final: 0.8623 (t0) REVERT: D 261 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8380 (p0) REVERT: D 297 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8785 (tm) REVERT: D 311 LYS cc_start: 0.8637 (tmtt) cc_final: 0.8175 (tmtt) REVERT: D 337 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7338 (tt) REVERT: D 386 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8212 (pmm) REVERT: D 420 MET cc_start: 0.7382 (mmm) cc_final: 0.6986 (mmm) REVERT: D 464 ILE cc_start: 0.8831 (pp) cc_final: 0.8563 (pp) REVERT: D 469 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.7686 (pt0) REVERT: D 470 ASP cc_start: 0.8691 (m-30) cc_final: 0.8266 (m-30) REVERT: D 488 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7560 (tp) REVERT: D 490 PHE cc_start: 0.8396 (m-80) cc_final: 0.7878 (m-80) REVERT: E 32 TYR cc_start: 0.8600 (m-10) cc_final: 0.8319 (m-10) REVERT: E 51 LEU cc_start: 0.8499 (mt) cc_final: 0.8217 (mt) REVERT: E 78 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7702 (ttt) REVERT: E 109 LYS cc_start: 0.8567 (mmtm) cc_final: 0.8345 (mptt) REVERT: E 165 PHE cc_start: 0.8093 (p90) cc_final: 0.7776 (p90) REVERT: E 166 LEU cc_start: 0.8128 (tp) cc_final: 0.7825 (tp) REVERT: E 185 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.8038 (mt) REVERT: E 206 LYS cc_start: 0.8162 (tppt) cc_final: 0.7851 (tppt) REVERT: E 216 ASP cc_start: 0.9128 (t70) cc_final: 0.8755 (t0) REVERT: E 250 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7714 (pp) REVERT: E 262 LEU cc_start: 0.9338 (tp) cc_final: 0.9074 (tp) REVERT: E 297 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8689 (tm) REVERT: E 311 LYS cc_start: 0.8666 (tmtt) cc_final: 0.8323 (ttpp) REVERT: E 337 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.6979 (tt) REVERT: E 361 VAL cc_start: 0.9392 (t) cc_final: 0.9178 (m) REVERT: E 386 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8265 (pmm) REVERT: E 390 LEU cc_start: 0.8899 (tt) cc_final: 0.8531 (tt) REVERT: E 407 ARG cc_start: 0.7372 (ttt180) cc_final: 0.7049 (tpt-90) REVERT: E 408 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8355 (mp) REVERT: E 420 MET cc_start: 0.7452 (mmm) cc_final: 0.6997 (mmm) REVERT: E 469 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.7660 (pt0) REVERT: E 470 ASP cc_start: 0.8642 (m-30) cc_final: 0.8334 (m-30) REVERT: E 509 TYR cc_start: 0.7555 (p90) cc_final: 0.7248 (p90) REVERT: E 510 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6986 (mm-30) REVERT: F 32 TYR cc_start: 0.8632 (m-10) cc_final: 0.8380 (m-10) REVERT: F 47 ASP cc_start: 0.9208 (m-30) cc_final: 0.8447 (p0) REVERT: F 65 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9051 (pt) REVERT: F 78 MET cc_start: 0.8108 (ttm) cc_final: 0.7435 (ttp) REVERT: F 109 LYS cc_start: 0.8658 (mmtm) cc_final: 0.8394 (mptt) REVERT: F 128 ARG cc_start: 0.8875 (mmt90) cc_final: 0.8636 (mmt180) REVERT: F 132 GLU cc_start: 0.9468 (mp0) cc_final: 0.9125 (mp0) REVERT: F 161 ARG cc_start: 0.9377 (mpp-170) cc_final: 0.8875 (mtt90) REVERT: F 165 PHE cc_start: 0.8512 (p90) cc_final: 0.7564 (p90) REVERT: F 166 LEU cc_start: 0.8257 (tp) cc_final: 0.7935 (tp) REVERT: F 206 LYS cc_start: 0.8124 (mtmt) cc_final: 0.7742 (ttpt) REVERT: F 216 ASP cc_start: 0.8991 (t70) cc_final: 0.8631 (t0) REVERT: F 235 LEU cc_start: 0.9040 (mt) cc_final: 0.8756 (mt) REVERT: F 261 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8311 (p0) REVERT: F 283 GLN cc_start: 0.8646 (tt0) cc_final: 0.8404 (mt0) REVERT: F 297 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8789 (tm) REVERT: F 311 LYS cc_start: 0.8721 (tmtt) cc_final: 0.8274 (tmtt) REVERT: F 337 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7204 (tt) REVERT: F 361 VAL cc_start: 0.9376 (t) cc_final: 0.9123 (m) REVERT: F 385 MET cc_start: 0.7208 (ttt) cc_final: 0.6578 (tpp) REVERT: F 386 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8031 (pmm) REVERT: F 466 HIS cc_start: 0.8298 (OUTLIER) cc_final: 0.7815 (t-90) REVERT: F 470 ASP cc_start: 0.8673 (m-30) cc_final: 0.8268 (m-30) REVERT: F 476 LEU cc_start: 0.8697 (mp) cc_final: 0.8488 (mp) REVERT: F 482 MET cc_start: 0.8710 (tpt) cc_final: 0.8450 (tpt) REVERT: F 490 PHE cc_start: 0.8465 (m-80) cc_final: 0.8173 (m-80) REVERT: F 510 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6877 (mm-30) REVERT: G 32 TYR cc_start: 0.8553 (m-10) cc_final: 0.8272 (m-10) REVERT: G 111 GLU cc_start: 0.8764 (mp0) cc_final: 0.8202 (pm20) REVERT: G 128 ARG cc_start: 0.8816 (mmt90) cc_final: 0.8490 (mmt90) REVERT: G 129 ASP cc_start: 0.9046 (m-30) cc_final: 0.8837 (m-30) REVERT: G 132 GLU cc_start: 0.9441 (mp0) cc_final: 0.9151 (mp0) REVERT: G 161 ARG cc_start: 0.9408 (mpp-170) cc_final: 0.9028 (mtt90) REVERT: G 165 PHE cc_start: 0.8097 (p90) cc_final: 0.7641 (p90) REVERT: G 166 LEU cc_start: 0.8156 (tp) cc_final: 0.7834 (tp) REVERT: G 216 ASP cc_start: 0.9107 (t70) cc_final: 0.8802 (t0) REVERT: G 277 GLN cc_start: 0.9072 (tm-30) cc_final: 0.8708 (tm-30) REVERT: G 297 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8720 (tm) REVERT: G 311 LYS cc_start: 0.8602 (tmtt) cc_final: 0.8246 (ttpp) REVERT: G 337 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7087 (tt) REVERT: G 352 GLU cc_start: 0.8747 (tp30) cc_final: 0.8465 (tp30) REVERT: G 386 MET cc_start: 0.8809 (ppp) cc_final: 0.8385 (pmm) REVERT: G 407 ARG cc_start: 0.7456 (ttt180) cc_final: 0.7166 (ttt90) REVERT: G 408 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8490 (mp) REVERT: G 420 MET cc_start: 0.7266 (mmm) cc_final: 0.6928 (mmm) REVERT: G 465 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7744 (mt0) REVERT: G 469 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.7757 (pt0) REVERT: G 470 ASP cc_start: 0.8685 (m-30) cc_final: 0.8375 (m-30) REVERT: G 489 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7972 (tttt) REVERT: G 490 PHE cc_start: 0.8380 (m-80) cc_final: 0.7988 (m-80) REVERT: G 510 GLU cc_start: 0.6950 (mm-30) cc_final: 0.6699 (mm-30) REVERT: H 62 LYS cc_start: 0.9260 (mmtp) cc_final: 0.8991 (mttm) REVERT: H 78 MET cc_start: 0.7453 (ttt) cc_final: 0.7172 (tmm) REVERT: H 165 PHE cc_start: 0.8009 (p90) cc_final: 0.7719 (p90) REVERT: H 166 LEU cc_start: 0.8098 (tp) cc_final: 0.7822 (tp) REVERT: H 199 GLU cc_start: 0.9453 (tp30) cc_final: 0.8824 (tp30) REVERT: H 202 GLN cc_start: 0.9326 (mm110) cc_final: 0.8990 (mm110) REVERT: H 203 ARG cc_start: 0.9294 (ptp-110) cc_final: 0.8951 (ptp-110) REVERT: H 208 LYS cc_start: 0.8363 (ttmm) cc_final: 0.7926 (mtmt) REVERT: H 216 ASP cc_start: 0.8999 (t70) cc_final: 0.8683 (t0) REVERT: H 250 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7814 (pp) REVERT: H 297 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8750 (tm) REVERT: H 311 LYS cc_start: 0.8703 (tmtt) cc_final: 0.8231 (tmtt) REVERT: H 337 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7048 (tt) REVERT: H 386 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.7987 (pmm) REVERT: H 469 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7516 (pt0) REVERT: H 470 ASP cc_start: 0.8673 (m-30) cc_final: 0.8341 (m-30) REVERT: H 488 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7825 (tp) REVERT: H 490 PHE cc_start: 0.8444 (m-80) cc_final: 0.8240 (m-80) REVERT: H 509 TYR cc_start: 0.7639 (p90) cc_final: 0.7342 (p90) outliers start: 232 outliers final: 171 residues processed: 1164 average time/residue: 0.1856 time to fit residues: 348.0826 Evaluate side-chains 1231 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 1011 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 493 ARG Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 466 HIS Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain G residue 465 GLN Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 222 ILE Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 469 GLN Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 494 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 353 optimal weight: 20.0000 chunk 240 optimal weight: 20.0000 chunk 300 optimal weight: 1.9990 chunk 176 optimal weight: 0.6980 chunk 383 optimal weight: 0.0770 chunk 59 optimal weight: 0.9990 chunk 351 optimal weight: 10.0000 chunk 206 optimal weight: 5.9990 chunk 197 optimal weight: 40.0000 chunk 261 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 overall best weight: 1.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN D 303 ASN ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 465 GLN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 GLN ** G 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 GLN H 283 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.170050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.131515 restraints weight = 51755.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.137279 restraints weight = 29829.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.141426 restraints weight = 20360.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.144254 restraints weight = 15273.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.146371 restraints weight = 12295.664| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 31592 Z= 0.188 Angle : 0.906 13.723 42888 Z= 0.439 Chirality : 0.051 0.249 4888 Planarity : 0.006 0.092 5328 Dihedral : 15.296 139.384 5334 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 7.46 % Allowed : 32.80 % Favored : 59.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -2.19 (0.13), residues: 3880 helix: -1.44 (0.13), residues: 1224 sheet: -2.43 (0.20), residues: 528 loop : -1.11 (0.14), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 355 TYR 0.029 0.002 TYR C 509 PHE 0.017 0.001 PHE C 90 HIS 0.008 0.001 HIS G 466 Details of bonding type rmsd covalent geometry : bond 0.00442 (31576) covalent geometry : angle 0.90586 (42888) hydrogen bonds : bond 0.03551 ( 832) hydrogen bonds : angle 5.43375 ( 2376) Misc. bond : bond 0.00028 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1235 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 997 time to evaluate : 1.131 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8509 (m-10) cc_final: 0.8263 (m-10) REVERT: A 51 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8052 (pp) REVERT: A 111 GLU cc_start: 0.8806 (mp0) cc_final: 0.8577 (mp0) REVERT: A 165 PHE cc_start: 0.8055 (p90) cc_final: 0.7773 (p90) REVERT: A 214 GLU cc_start: 0.9298 (mm-30) cc_final: 0.9068 (mp0) REVERT: A 216 ASP cc_start: 0.9014 (t70) cc_final: 0.8725 (t0) REVERT: A 250 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8117 (pp) REVERT: A 311 LYS cc_start: 0.8668 (tmtt) cc_final: 0.8309 (ttpp) REVERT: A 337 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7161 (tt) REVERT: A 352 GLU cc_start: 0.8638 (tp30) cc_final: 0.8308 (tp30) REVERT: A 361 VAL cc_start: 0.9334 (t) cc_final: 0.9047 (m) REVERT: A 386 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8188 (ppp) REVERT: A 469 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.7951 (pt0) REVERT: A 470 ASP cc_start: 0.8569 (m-30) cc_final: 0.8293 (m-30) REVERT: A 490 PHE cc_start: 0.8456 (m-80) cc_final: 0.8083 (m-80) REVERT: A 509 TYR cc_start: 0.7448 (p90) cc_final: 0.7092 (p90) REVERT: A 510 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6780 (mm-30) REVERT: B 32 TYR cc_start: 0.8626 (m-10) cc_final: 0.8359 (m-10) REVERT: B 109 LYS cc_start: 0.8698 (mmtm) cc_final: 0.8464 (mptt) REVERT: B 128 ARG cc_start: 0.9075 (mmm-85) cc_final: 0.8854 (mmm-85) REVERT: B 202 GLN cc_start: 0.9375 (mm-40) cc_final: 0.9093 (mm-40) REVERT: B 216 ASP cc_start: 0.9002 (t70) cc_final: 0.8633 (t0) REVERT: B 250 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7755 (pp) REVERT: B 261 ASP cc_start: 0.8611 (p0) cc_final: 0.8280 (p0) REVERT: B 283 GLN cc_start: 0.8601 (tt0) cc_final: 0.8339 (mt0) REVERT: B 311 LYS cc_start: 0.8749 (tmtt) cc_final: 0.8280 (tmtt) REVERT: B 337 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7255 (tt) REVERT: B 385 MET cc_start: 0.7703 (ttt) cc_final: 0.7491 (ttt) REVERT: B 386 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.7893 (ppp) REVERT: B 420 MET cc_start: 0.7412 (mmm) cc_final: 0.6621 (mmt) REVERT: B 469 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.7790 (pt0) REVERT: B 470 ASP cc_start: 0.8749 (m-30) cc_final: 0.8416 (m-30) REVERT: B 482 MET cc_start: 0.8621 (tpt) cc_final: 0.8376 (tpt) REVERT: B 490 PHE cc_start: 0.8530 (m-80) cc_final: 0.8171 (m-80) REVERT: C 32 TYR cc_start: 0.8633 (m-10) cc_final: 0.8210 (m-10) REVERT: C 62 LYS cc_start: 0.9006 (mmtp) cc_final: 0.8516 (mtpt) REVERT: C 128 ARG cc_start: 0.8869 (mmt90) cc_final: 0.8655 (mmt90) REVERT: C 129 ASP cc_start: 0.9091 (m-30) cc_final: 0.8873 (m-30) REVERT: C 132 GLU cc_start: 0.9429 (mp0) cc_final: 0.9126 (mp0) REVERT: C 179 MET cc_start: 0.7707 (ptm) cc_final: 0.7466 (ptm) REVERT: C 214 GLU cc_start: 0.9292 (mm-30) cc_final: 0.9027 (mp0) REVERT: C 216 ASP cc_start: 0.9102 (t70) cc_final: 0.8747 (t0) REVERT: C 250 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.7895 (pp) REVERT: C 297 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8818 (tm) REVERT: C 311 LYS cc_start: 0.8608 (tmtt) cc_final: 0.8241 (ttpp) REVERT: C 337 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7115 (tt) REVERT: C 348 TYR cc_start: 0.9124 (t80) cc_final: 0.8898 (t80) REVERT: C 352 GLU cc_start: 0.8806 (tp30) cc_final: 0.8406 (tp30) REVERT: C 420 MET cc_start: 0.7348 (mmm) cc_final: 0.6411 (mmt) REVERT: C 469 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.7762 (pt0) REVERT: C 490 PHE cc_start: 0.8426 (m-80) cc_final: 0.7972 (m-80) REVERT: C 510 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.7032 (mm-30) REVERT: D 32 TYR cc_start: 0.8611 (m-10) cc_final: 0.8175 (m-10) REVERT: D 109 LYS cc_start: 0.8582 (mmtm) cc_final: 0.8226 (mmmm) REVERT: D 128 ARG cc_start: 0.8900 (mmt90) cc_final: 0.8521 (mmt90) REVERT: D 165 PHE cc_start: 0.8061 (p90) cc_final: 0.7722 (p90) REVERT: D 166 LEU cc_start: 0.8298 (tp) cc_final: 0.7976 (tp) REVERT: D 179 MET cc_start: 0.6772 (pmm) cc_final: 0.6205 (pmm) REVERT: D 199 GLU cc_start: 0.9464 (tp30) cc_final: 0.9032 (tp30) REVERT: D 202 GLN cc_start: 0.9400 (mm-40) cc_final: 0.8974 (mm-40) REVERT: D 203 ARG cc_start: 0.9337 (ptp-110) cc_final: 0.9096 (ptp-110) REVERT: D 216 ASP cc_start: 0.9019 (t70) cc_final: 0.8654 (t0) REVERT: D 261 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8406 (p0) REVERT: D 265 GLN cc_start: 0.9294 (mm110) cc_final: 0.9059 (mm-40) REVERT: D 297 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8870 (tm) REVERT: D 311 LYS cc_start: 0.8667 (tmtt) cc_final: 0.8207 (tmtt) REVERT: D 337 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7421 (tt) REVERT: D 386 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8145 (pmm) REVERT: D 420 MET cc_start: 0.7386 (mmm) cc_final: 0.6950 (mmm) REVERT: D 464 ILE cc_start: 0.8927 (pp) cc_final: 0.8675 (pp) REVERT: D 469 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.7820 (pt0) REVERT: D 470 ASP cc_start: 0.8706 (m-30) cc_final: 0.8321 (m-30) REVERT: D 482 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8406 (tpt) REVERT: D 487 GLU cc_start: 0.8390 (pm20) cc_final: 0.7624 (pm20) REVERT: D 488 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7593 (tp) REVERT: D 490 PHE cc_start: 0.8437 (m-80) cc_final: 0.7905 (m-80) REVERT: E 32 TYR cc_start: 0.8638 (m-10) cc_final: 0.8339 (m-10) REVERT: E 78 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7759 (ttt) REVERT: E 111 GLU cc_start: 0.8778 (mp0) cc_final: 0.8274 (pm20) REVERT: E 132 GLU cc_start: 0.9435 (mp0) cc_final: 0.9064 (mp0) REVERT: E 165 PHE cc_start: 0.8145 (p90) cc_final: 0.7834 (p90) REVERT: E 179 MET cc_start: 0.7749 (ptm) cc_final: 0.7464 (mtm) REVERT: E 185 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7856 (mt) REVERT: E 206 LYS cc_start: 0.8275 (tppt) cc_final: 0.8047 (tppt) REVERT: E 216 ASP cc_start: 0.9152 (t70) cc_final: 0.8769 (t0) REVERT: E 224 ARG cc_start: 0.8841 (ttt180) cc_final: 0.8629 (ttm170) REVERT: E 250 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7811 (pp) REVERT: E 297 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8736 (tm) REVERT: E 311 LYS cc_start: 0.8700 (tmtt) cc_final: 0.8318 (ttpp) REVERT: E 337 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7122 (tt) REVERT: E 386 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8364 (pmm) REVERT: E 390 LEU cc_start: 0.8944 (tt) cc_final: 0.8588 (tt) REVERT: E 408 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8443 (mp) REVERT: E 420 MET cc_start: 0.7445 (mmm) cc_final: 0.6977 (mmm) REVERT: E 469 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.7721 (pt0) REVERT: E 470 ASP cc_start: 0.8651 (m-30) cc_final: 0.8341 (m-30) REVERT: E 476 LEU cc_start: 0.8544 (mp) cc_final: 0.8227 (mt) REVERT: E 509 TYR cc_start: 0.7584 (p90) cc_final: 0.7277 (p90) REVERT: E 510 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6725 (mm-30) REVERT: F 32 TYR cc_start: 0.8653 (m-10) cc_final: 0.8397 (m-10) REVERT: F 47 ASP cc_start: 0.9203 (m-30) cc_final: 0.8426 (p0) REVERT: F 65 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9054 (pt) REVERT: F 66 VAL cc_start: 0.8770 (OUTLIER) cc_final: 0.8374 (p) REVERT: F 78 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7422 (ttp) REVERT: F 109 LYS cc_start: 0.8679 (mmtm) cc_final: 0.8327 (mptt) REVERT: F 128 ARG cc_start: 0.8887 (mmt90) cc_final: 0.8653 (mmt90) REVERT: F 132 GLU cc_start: 0.9466 (mp0) cc_final: 0.9135 (mp0) REVERT: F 161 ARG cc_start: 0.9415 (mpp-170) cc_final: 0.8958 (mtt90) REVERT: F 166 LEU cc_start: 0.8271 (tp) cc_final: 0.7926 (tp) REVERT: F 179 MET cc_start: 0.6854 (pmm) cc_final: 0.6404 (pmm) REVERT: F 216 ASP cc_start: 0.9031 (t70) cc_final: 0.8665 (t0) REVERT: F 261 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8381 (p0) REVERT: F 262 LEU cc_start: 0.9123 (tt) cc_final: 0.8889 (tp) REVERT: F 283 GLN cc_start: 0.8730 (tt0) cc_final: 0.8497 (mt0) REVERT: F 297 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8797 (tm) REVERT: F 311 LYS cc_start: 0.8729 (tmtt) cc_final: 0.8265 (tmtt) REVERT: F 337 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7257 (tt) REVERT: F 352 GLU cc_start: 0.8810 (tp30) cc_final: 0.8473 (tp30) REVERT: F 361 VAL cc_start: 0.9427 (t) cc_final: 0.9195 (m) REVERT: F 386 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8196 (pmm) REVERT: F 466 HIS cc_start: 0.8360 (OUTLIER) cc_final: 0.7562 (t-90) REVERT: F 469 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.7818 (pt0) REVERT: F 470 ASP cc_start: 0.8677 (m-30) cc_final: 0.8232 (m-30) REVERT: F 476 LEU cc_start: 0.8704 (mp) cc_final: 0.8458 (mp) REVERT: F 482 MET cc_start: 0.8737 (tpt) cc_final: 0.8486 (tpt) REVERT: F 488 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7599 (tp) REVERT: F 490 PHE cc_start: 0.8480 (m-80) cc_final: 0.8258 (m-80) REVERT: F 510 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6619 (mm-30) REVERT: G 32 TYR cc_start: 0.8608 (m-10) cc_final: 0.8283 (m-10) REVERT: G 66 VAL cc_start: 0.8848 (OUTLIER) cc_final: 0.8564 (p) REVERT: G 128 ARG cc_start: 0.8803 (mmt90) cc_final: 0.8480 (mmt90) REVERT: G 129 ASP cc_start: 0.9065 (m-30) cc_final: 0.8847 (m-30) REVERT: G 132 GLU cc_start: 0.9420 (mp0) cc_final: 0.9120 (mp0) REVERT: G 165 PHE cc_start: 0.8131 (p90) cc_final: 0.7675 (p90) REVERT: G 166 LEU cc_start: 0.8166 (tp) cc_final: 0.7849 (tp) REVERT: G 216 ASP cc_start: 0.9135 (t70) cc_final: 0.8844 (t0) REVERT: G 277 GLN cc_start: 0.9126 (tm-30) cc_final: 0.8714 (tm-30) REVERT: G 297 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8786 (tm) REVERT: G 311 LYS cc_start: 0.8631 (tmtt) cc_final: 0.8292 (ttpp) REVERT: G 337 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7246 (tt) REVERT: G 352 GLU cc_start: 0.8756 (tp30) cc_final: 0.8505 (tp30) REVERT: G 386 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8512 (pmm) REVERT: G 407 ARG cc_start: 0.7486 (ttt180) cc_final: 0.7252 (ttt180) REVERT: G 420 MET cc_start: 0.7394 (mmm) cc_final: 0.7022 (mmm) REVERT: G 465 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7604 (mt0) REVERT: G 469 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.7442 (pt0) REVERT: G 470 ASP cc_start: 0.8763 (m-30) cc_final: 0.8412 (m-30) REVERT: G 489 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.8014 (tttt) REVERT: G 490 PHE cc_start: 0.8424 (m-80) cc_final: 0.7964 (m-80) REVERT: G 509 TYR cc_start: 0.7557 (p90) cc_final: 0.7200 (p90) REVERT: H 62 LYS cc_start: 0.9290 (mmtp) cc_final: 0.9022 (mttm) REVERT: H 78 MET cc_start: 0.7592 (ttt) cc_final: 0.7326 (tmm) REVERT: H 165 PHE cc_start: 0.8023 (p90) cc_final: 0.7745 (p90) REVERT: H 199 GLU cc_start: 0.9467 (tp30) cc_final: 0.9156 (tp30) REVERT: H 202 GLN cc_start: 0.9402 (OUTLIER) cc_final: 0.9080 (mm110) REVERT: H 203 ARG cc_start: 0.9273 (ptp-110) cc_final: 0.9033 (ptp-110) REVERT: H 208 LYS cc_start: 0.8374 (ttmm) cc_final: 0.7918 (mtmt) REVERT: H 216 ASP cc_start: 0.9022 (t70) cc_final: 0.8704 (t0) REVERT: H 250 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.7898 (pp) REVERT: H 297 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8812 (tm) REVERT: H 311 LYS cc_start: 0.8720 (tmtt) cc_final: 0.8247 (tmtt) REVERT: H 337 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7166 (tt) REVERT: H 361 VAL cc_start: 0.9457 (t) cc_final: 0.9239 (m) REVERT: H 386 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8076 (pmm) REVERT: H 469 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.7661 (pt0) REVERT: H 470 ASP cc_start: 0.8639 (m-30) cc_final: 0.8359 (m-30) REVERT: H 490 PHE cc_start: 0.8522 (m-80) cc_final: 0.8119 (m-80) REVERT: H 509 TYR cc_start: 0.7569 (p90) cc_final: 0.7353 (p90) outliers start: 238 outliers final: 166 residues processed: 1108 average time/residue: 0.1956 time to fit residues: 349.3062 Evaluate side-chains 1182 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 961 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 353 TYR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 493 ARG Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 466 HIS Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain G residue 465 GLN Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 222 ILE Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 353 TYR Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 469 GLN Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 494 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 56 optimal weight: 3.9990 chunk 273 optimal weight: 0.9980 chunk 220 optimal weight: 6.9990 chunk 314 optimal weight: 5.9990 chunk 234 optimal weight: 3.9990 chunk 377 optimal weight: 0.2980 chunk 162 optimal weight: 1.9990 chunk 214 optimal weight: 0.4980 chunk 235 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN A 312 ASN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN G 469 GLN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.168275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.132592 restraints weight = 51464.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.138259 restraints weight = 29167.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.142188 restraints weight = 19620.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.144933 restraints weight = 14550.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.146847 restraints weight = 11566.055| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31592 Z= 0.153 Angle : 0.909 14.740 42888 Z= 0.436 Chirality : 0.051 0.244 4888 Planarity : 0.005 0.086 5328 Dihedral : 15.201 139.701 5330 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 7.02 % Allowed : 33.46 % Favored : 59.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -2.19 (0.13), residues: 3880 helix: -1.41 (0.13), residues: 1216 sheet: -2.45 (0.20), residues: 528 loop : -1.11 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 480 TYR 0.030 0.002 TYR D 509 PHE 0.013 0.001 PHE H 402 HIS 0.007 0.001 HIS G 466 Details of bonding type rmsd covalent geometry : bond 0.00360 (31576) covalent geometry : angle 0.90884 (42888) hydrogen bonds : bond 0.03453 ( 832) hydrogen bonds : angle 5.38755 ( 2376) Misc. bond : bond 0.00035 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7273.94 seconds wall clock time: 126 minutes 21.76 seconds (7581.76 seconds total)