Starting phenix.real_space_refine on Mon Jul 6 00:42:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uaj_20707/07_2026/6uaj_20707.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uaj_20707/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6uaj_20707/07_2026/6uaj_20707.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uaj_20707/07_2026/6uaj_20707.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uaj_20707/07_2026/6uaj_20707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uaj_20707/07_2026/6uaj_20707.map" model { file = "/net/cci-nas-00/data/ceres_data/6uaj_20707/07_2026/6uaj_20707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uaj_20707/07_2026/6uaj_20707.cif" } 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-6108/lib/python3.11/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: 5.88, per 1000 atoms: 0.19 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: 2.08 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: 0.96 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: 5.58 Time building geometry restraints manager: 2.82 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: 17924 34.54 - 69.09: 696 69.09 - 103.63: 60 103.63 - 138.18: 8 138.18 - 172.72: 32 Dihedral angle restraints: 18720 sinusoidal: 7600 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 18717 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: 0.06 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 25.620 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 : 19.094 172.723 11616 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/Z covalent geometry : bond 0.01809 / 1.00 (31576) covalent geometry : angle 1.86090 / 1.02 (42888) hydrogen bonds : bond 0.19900 / 13.59 ( 832) hydrogen bonds : angle 7.99348 / 5.39 ( 2376) Misc. bond : bond 0.00044 / 0.03 ( 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 : 1.037 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: 0.2062 time to fit residues: 487.9344 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 : 1.115 ------------------------------------------------------------------------------- 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... ** 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 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 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.167139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.129288 restraints weight = 50375.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.134851 restraints weight = 28933.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.138729 restraints weight = 19689.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.141483 restraints weight = 14789.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.143612 restraints weight = 11866.365| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31592 Z= 0.168 Angle : 0.846 10.221 42888 Z= 0.418 Chirality : 0.050 0.167 4888 Planarity : 0.005 0.041 5328 Dihedral : 19.464 161.960 4954 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 7.74 % Allowed : 22.78 % Favored : 69.49 % 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: -3.09 (0.12), residues: 3880 helix: -2.13 (0.12), residues: 1224 sheet: -2.72 (0.18), residues: 520 loop : -1.78 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 149 TYR 0.023 0.002 TYR H 484 PHE 0.018 0.002 PHE B 456 HIS 0.005 0.001 HIS D 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (31576) covalent geometry : angle 0.84554 / 0.42 (42888) hydrogen bonds : bond 0.04969 / 3.29 ( 832) hydrogen bonds : angle 6.03977 / 4.16 ( 2376) Misc. bond : bond 0.00069 / 0.05 ( 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 1344 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 247 poor density : 1097 time to evaluate : 1.152 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: A 32 TYR cc_start: 0.8659 (m-80) cc_final: 0.8350 (m-10) REVERT: A 73 VAL cc_start: 0.8272 (OUTLIER) cc_final: 0.6654 (t) REVERT: A 136 ARG cc_start: 0.8989 (ptp-110) cc_final: 0.8571 (ptp90) REVERT: A 165 PHE cc_start: 0.8242 (p90) cc_final: 0.8030 (p90) REVERT: A 202 GLN cc_start: 0.9300 (mt0) cc_final: 0.8898 (mt0) REVERT: A 206 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7992 (ttmm) REVERT: A 250 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7854 (pp) REVERT: A 254 GLU cc_start: 0.9345 (pp20) cc_final: 0.9129 (pm20) REVERT: A 285 ASN cc_start: 0.9464 (m110) cc_final: 0.9144 (m110) REVERT: A 297 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8700 (tm) REVERT: A 311 LYS cc_start: 0.8746 (tmtt) cc_final: 0.8314 (tptt) REVERT: A 352 GLU cc_start: 0.8618 (tp30) cc_final: 0.8392 (tp30) REVERT: A 379 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9246 (tm) REVERT: A 386 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8358 (ppp) REVERT: A 407 ARG cc_start: 0.7414 (ttt180) cc_final: 0.7078 (ttt90) REVERT: A 420 MET cc_start: 0.6567 (mmm) cc_final: 0.6082 (mmm) REVERT: A 466 HIS cc_start: 0.8962 (OUTLIER) cc_final: 0.8248 (t-90) REVERT: A 470 ASP cc_start: 0.8511 (m-30) cc_final: 0.8103 (m-30) REVERT: A 482 MET cc_start: 0.8507 (tpt) cc_final: 0.8140 (tpt) REVERT: A 487 GLU cc_start: 0.8530 (pm20) cc_final: 0.8028 (pm20) REVERT: A 490 PHE cc_start: 0.8262 (m-80) cc_final: 0.7848 (m-80) REVERT: A 509 TYR cc_start: 0.7763 (p90) cc_final: 0.7495 (p90) REVERT: A 510 GLU cc_start: 0.6653 (mm-30) cc_final: 0.6425 (mm-30) REVERT: A 514 PHE cc_start: 0.7194 (p90) cc_final: 0.6479 (p90) REVERT: B 161 ARG cc_start: 0.9534 (mpp-170) cc_final: 0.9074 (mtt90) REVERT: B 165 PHE cc_start: 0.7952 (p90) cc_final: 0.7680 (p90) REVERT: B 180 THR cc_start: 0.8164 (p) cc_final: 0.7799 (t) REVERT: B 199 GLU cc_start: 0.9312 (tp30) cc_final: 0.8916 (tp30) REVERT: B 202 GLN cc_start: 0.9331 (mt0) cc_final: 0.8974 (mt0) REVERT: B 203 ARG cc_start: 0.9013 (ptp-110) cc_final: 0.8806 (ptp-110) REVERT: B 206 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8139 (ttpt) REVERT: B 208 LYS cc_start: 0.8317 (mtpp) cc_final: 0.8068 (ttmm) REVERT: B 214 GLU cc_start: 0.9307 (mm-30) cc_final: 0.9086 (mp0) REVERT: B 216 ASP cc_start: 0.8956 (t70) cc_final: 0.8612 (t0) REVERT: B 232 ASP cc_start: 0.9270 (t0) cc_final: 0.9020 (t0) REVERT: B 233 TYR cc_start: 0.8990 (m-80) cc_final: 0.8723 (m-80) REVERT: B 239 ASP cc_start: 0.8822 (p0) cc_final: 0.8102 (p0) REVERT: B 243 GLN cc_start: 0.8616 (mp10) cc_final: 0.8310 (mp10) REVERT: B 258 TYR cc_start: 0.8353 (t80) cc_final: 0.8050 (t80) REVERT: B 285 ASN cc_start: 0.9342 (m110) cc_final: 0.9101 (m110) REVERT: B 297 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8725 (tm) REVERT: B 311 LYS cc_start: 0.8895 (tmtt) cc_final: 0.8315 (tptt) REVERT: B 385 MET cc_start: 0.8590 (ttp) cc_final: 0.8372 (ttp) REVERT: B 386 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8303 (ppp) REVERT: B 399 GLU cc_start: 0.7251 (pp20) cc_final: 0.7011 (pp20) REVERT: B 400 TYR cc_start: 0.7895 (m-80) cc_final: 0.7411 (m-80) REVERT: B 401 PHE cc_start: 0.8278 (p90) cc_final: 0.8057 (p90) REVERT: B 441 GLN cc_start: 0.8389 (mm-40) cc_final: 0.8186 (mm-40) REVERT: B 482 MET cc_start: 0.8503 (tpt) cc_final: 0.8146 (tpt) REVERT: B 487 GLU cc_start: 0.8528 (pm20) cc_final: 0.8157 (pm20) REVERT: B 490 PHE cc_start: 0.8399 (m-80) cc_final: 0.7969 (m-80) REVERT: B 514 PHE cc_start: 0.7165 (p90) cc_final: 0.6915 (p90) REVERT: C 32 TYR cc_start: 0.8666 (m-80) cc_final: 0.8385 (m-10) REVERT: C 78 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.8035 (ttp) REVERT: C 199 GLU cc_start: 0.9327 (tp30) cc_final: 0.9030 (tp30) REVERT: C 202 GLN cc_start: 0.9334 (mt0) cc_final: 0.8938 (mt0) REVERT: C 206 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8092 (ttpt) REVERT: C 208 LYS cc_start: 0.8441 (mtpp) cc_final: 0.8190 (ttmm) REVERT: C 250 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7576 (pp) REVERT: C 261 ASP cc_start: 0.8902 (m-30) cc_final: 0.8667 (p0) REVERT: C 285 ASN cc_start: 0.9381 (m110) cc_final: 0.9067 (m110) REVERT: C 297 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8689 (tm) REVERT: C 311 LYS cc_start: 0.8824 (tmtt) cc_final: 0.8354 (tptt) REVERT: C 357 PHE cc_start: 0.8869 (m-80) cc_final: 0.8510 (m-10) REVERT: C 386 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8403 (ppp) REVERT: C 407 ARG cc_start: 0.7404 (ttt180) cc_final: 0.6800 (ttt90) REVERT: C 420 MET cc_start: 0.6434 (mmm) cc_final: 0.6002 (mmm) REVERT: C 466 HIS cc_start: 0.9047 (OUTLIER) cc_final: 0.8258 (t-90) REVERT: C 470 ASP cc_start: 0.8527 (m-30) cc_final: 0.8077 (m-30) REVERT: C 482 MET cc_start: 0.8554 (tpt) cc_final: 0.8205 (tpt) REVERT: C 487 GLU cc_start: 0.8580 (pm20) cc_final: 0.8201 (pm20) REVERT: C 490 PHE cc_start: 0.8297 (m-80) cc_final: 0.7959 (m-80) REVERT: C 514 PHE cc_start: 0.7240 (p90) cc_final: 0.6993 (p90) REVERT: D 32 TYR cc_start: 0.8614 (m-10) cc_final: 0.8393 (m-10) REVERT: D 73 VAL cc_start: 0.8150 (OUTLIER) cc_final: 0.6372 (t) REVERT: D 78 MET cc_start: 0.8357 (ttm) cc_final: 0.8032 (ttp) REVERT: D 161 ARG cc_start: 0.9565 (mpp-170) cc_final: 0.9206 (mpt-90) REVERT: D 165 PHE cc_start: 0.8004 (p90) cc_final: 0.7727 (p90) REVERT: D 180 THR cc_start: 0.8447 (p) cc_final: 0.8038 (t) REVERT: D 199 GLU cc_start: 0.9508 (tp30) cc_final: 0.9219 (tp30) REVERT: D 206 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7996 (ttpt) REVERT: D 216 ASP cc_start: 0.8985 (t70) cc_final: 0.8651 (t0) REVERT: D 233 TYR cc_start: 0.9000 (m-80) cc_final: 0.8737 (m-80) REVERT: D 273 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8495 (mm) REVERT: D 297 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8784 (tm) REVERT: D 311 LYS cc_start: 0.8892 (tmtt) cc_final: 0.8456 (tptt) REVERT: D 385 MET cc_start: 0.8628 (ttp) cc_final: 0.8361 (ttp) REVERT: D 386 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8314 (ppp) REVERT: D 399 GLU cc_start: 0.7271 (pp20) cc_final: 0.7071 (pp20) REVERT: D 407 ARG cc_start: 0.7464 (ttt180) cc_final: 0.7204 (ttt180) REVERT: D 461 ILE cc_start: 0.9091 (pp) cc_final: 0.8663 (pt) REVERT: D 482 MET cc_start: 0.8606 (tpt) cc_final: 0.8228 (tpt) REVERT: D 484 TYR cc_start: 0.9060 (m-10) cc_final: 0.8158 (m-10) REVERT: D 487 GLU cc_start: 0.8565 (pm20) cc_final: 0.8191 (pm20) REVERT: D 490 PHE cc_start: 0.8348 (m-80) cc_final: 0.7945 (m-80) REVERT: E 32 TYR cc_start: 0.8621 (m-10) cc_final: 0.8354 (m-10) REVERT: E 78 MET cc_start: 0.8454 (ttm) cc_final: 0.8227 (ttt) REVERT: E 128 ARG cc_start: 0.8867 (mmt90) cc_final: 0.8349 (mmt90) REVERT: E 165 PHE cc_start: 0.8127 (p90) cc_final: 0.7687 (p90) REVERT: E 185 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7567 (mt) REVERT: E 199 GLU cc_start: 0.9531 (tp30) cc_final: 0.9267 (tp30) REVERT: E 206 LYS cc_start: 0.7956 (tppt) cc_final: 0.7623 (tppt) REVERT: E 216 ASP cc_start: 0.9015 (t70) cc_final: 0.8659 (t0) REVERT: E 250 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7568 (pp) REVERT: E 258 TYR cc_start: 0.8604 (t80) cc_final: 0.8339 (t80) REVERT: E 285 ASN cc_start: 0.9348 (m110) cc_final: 0.9044 (m110) REVERT: E 297 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8732 (tm) REVERT: E 311 LYS cc_start: 0.8863 (tmtt) cc_final: 0.8433 (tptt) REVERT: E 385 MET cc_start: 0.8463 (ttp) cc_final: 0.8029 (ttp) REVERT: E 386 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8317 (ppp) REVERT: E 420 MET cc_start: 0.6509 (mmm) cc_final: 0.6118 (mmm) REVERT: E 466 HIS cc_start: 0.9149 (OUTLIER) cc_final: 0.8357 (t-90) REVERT: E 482 MET cc_start: 0.8529 (tpt) cc_final: 0.8194 (tpt) REVERT: E 487 GLU cc_start: 0.8599 (pm20) cc_final: 0.8226 (pm20) REVERT: E 490 PHE cc_start: 0.8407 (m-80) cc_final: 0.8041 (m-80) REVERT: F 78 MET cc_start: 0.8459 (ttm) cc_final: 0.8236 (ttt) REVERT: F 109 LYS cc_start: 0.8656 (mmtm) cc_final: 0.8402 (mmtm) REVERT: F 165 PHE cc_start: 0.8163 (p90) cc_final: 0.7633 (p90) REVERT: F 180 THR cc_start: 0.8230 (p) cc_final: 0.7886 (t) REVERT: F 199 GLU cc_start: 0.9517 (tp30) cc_final: 0.9248 (tp30) REVERT: F 206 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8068 (ttpt) REVERT: F 216 ASP cc_start: 0.9018 (t70) cc_final: 0.8675 (t0) REVERT: F 258 TYR cc_start: 0.8371 (t80) cc_final: 0.8018 (t80) REVERT: F 285 ASN cc_start: 0.9337 (m110) cc_final: 0.9068 (m110) REVERT: F 297 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8718 (tm) REVERT: F 311 LYS cc_start: 0.8861 (tmtt) cc_final: 0.8426 (tptt) REVERT: F 312 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8368 (t0) REVERT: F 386 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8259 (ppp) REVERT: F 400 TYR cc_start: 0.7947 (m-80) cc_final: 0.7392 (m-80) REVERT: F 401 PHE cc_start: 0.8270 (p90) cc_final: 0.8008 (p90) REVERT: F 466 HIS cc_start: 0.9059 (OUTLIER) cc_final: 0.8308 (t-90) REVERT: F 482 MET cc_start: 0.8576 (tpt) cc_final: 0.8232 (tpt) REVERT: F 487 GLU cc_start: 0.8639 (pm20) cc_final: 0.8279 (pm20) REVERT: F 490 PHE cc_start: 0.8445 (m-80) cc_final: 0.8027 (m-80) REVERT: F 514 PHE cc_start: 0.7284 (p90) cc_final: 0.7012 (p90) REVERT: G 32 TYR cc_start: 0.8627 (m-80) cc_final: 0.8401 (m-10) REVERT: G 73 VAL cc_start: 0.8368 (OUTLIER) cc_final: 0.6784 (t) REVERT: G 109 LYS cc_start: 0.8755 (mmtm) cc_final: 0.8495 (mmtm) REVERT: G 165 PHE cc_start: 0.8086 (p90) cc_final: 0.7844 (p90) REVERT: G 179 MET cc_start: 0.7765 (ptm) cc_final: 0.7505 (ptt) REVERT: G 199 GLU cc_start: 0.9528 (tp30) cc_final: 0.9233 (tp30) REVERT: G 285 ASN cc_start: 0.9391 (m110) cc_final: 0.9062 (m110) REVERT: G 297 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8737 (tm) REVERT: G 311 LYS cc_start: 0.8850 (tmtt) cc_final: 0.8423 (tptt) REVERT: G 379 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9253 (tm) REVERT: G 385 MET cc_start: 0.8458 (ttp) cc_final: 0.8046 (ttt) REVERT: G 386 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8320 (ppp) REVERT: G 420 MET cc_start: 0.6520 (mmm) cc_final: 0.6151 (mmm) REVERT: G 441 GLN cc_start: 0.8398 (mm-40) cc_final: 0.8146 (mm-40) REVERT: G 466 HIS cc_start: 0.9062 (OUTLIER) cc_final: 0.8313 (t-90) REVERT: G 470 ASP cc_start: 0.8473 (m-30) cc_final: 0.8053 (m-30) REVERT: G 482 MET cc_start: 0.8594 (tpt) cc_final: 0.8249 (tpt) REVERT: G 487 GLU cc_start: 0.8630 (pm20) cc_final: 0.8268 (pm20) REVERT: G 490 PHE cc_start: 0.8408 (m-80) cc_final: 0.8063 (m-80) REVERT: G 509 TYR cc_start: 0.7893 (p90) cc_final: 0.7636 (p90) REVERT: G 510 GLU cc_start: 0.6750 (mm-30) cc_final: 0.6435 (mm-30) REVERT: H 32 TYR cc_start: 0.8572 (m-10) cc_final: 0.7933 (m-10) REVERT: H 136 ARG cc_start: 0.9018 (ptp-110) cc_final: 0.8681 (ptp90) REVERT: H 165 PHE cc_start: 0.8100 (p90) cc_final: 0.7605 (p90) REVERT: H 180 THR cc_start: 0.8205 (p) cc_final: 0.7924 (t) REVERT: H 199 GLU cc_start: 0.9501 (tp30) cc_final: 0.9244 (tp30) REVERT: H 206 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8091 (ttmm) REVERT: H 216 ASP cc_start: 0.8836 (t70) cc_final: 0.8475 (t0) REVERT: H 232 ASP cc_start: 0.9304 (t0) cc_final: 0.9097 (t0) REVERT: H 233 TYR cc_start: 0.8970 (m-80) cc_final: 0.8690 (m-80) REVERT: H 285 ASN cc_start: 0.9467 (m110) cc_final: 0.9121 (m110) REVERT: H 297 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8695 (tm) REVERT: H 311 LYS cc_start: 0.8809 (tmtt) cc_final: 0.8369 (tptt) REVERT: H 386 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8191 (pmm) REVERT: H 390 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8732 (tt) REVERT: H 400 TYR cc_start: 0.7876 (m-80) cc_final: 0.7454 (m-80) REVERT: H 401 PHE cc_start: 0.8269 (p90) cc_final: 0.8029 (p90) REVERT: H 441 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8320 (mm-40) REVERT: H 482 MET cc_start: 0.8495 (tpt) cc_final: 0.8125 (tpt) REVERT: H 484 TYR cc_start: 0.9015 (m-10) cc_final: 0.8155 (m-10) REVERT: H 487 GLU cc_start: 0.8608 (pm20) cc_final: 0.8170 (pm20) REVERT: H 490 PHE cc_start: 0.8276 (m-80) cc_final: 0.7884 (m-80) REVERT: H 514 PHE cc_start: 0.7271 (p90) cc_final: 0.6993 (p90) outliers start: 247 outliers final: 113 residues processed: 1189 average time/residue: 0.1897 time to fit residues: 365.7953 Evaluate side-chains 1080 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 927 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 73 VAL Chi-restraints excluded: chain A residue 74 THR 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 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 466 HIS 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 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 222 ILE 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 382 SER Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 466 HIS 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 312 ASN Chi-restraints excluded: chain F residue 370 VAL 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 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 297 LEU Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 306 THR 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: 9.9990 chunk 73 optimal weight: 4.9990 chunk 59 optimal weight: 20.0000 chunk 275 optimal weight: 0.3980 chunk 225 optimal weight: 0.0980 chunk 171 optimal weight: 3.9990 chunk 299 optimal weight: 20.0000 chunk 325 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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 230 ASN 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 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** 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 230 ASN 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 ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.165521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.125412 restraints weight = 51656.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.131005 restraints weight = 30018.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.134957 restraints weight = 20687.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.137765 restraints weight = 15719.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.139887 restraints weight = 12769.706| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 31592 Z= 0.228 Angle : 0.839 14.109 42888 Z= 0.415 Chirality : 0.050 0.178 4888 Planarity : 0.005 0.050 5328 Dihedral : 18.462 177.388 4727 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 9.34 % Allowed : 24.25 % Favored : 66.42 % 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: -1.84 (0.13), residues: 1296 sheet: -2.31 (0.19), residues: 512 loop : -1.34 (0.14), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 149 TYR 0.031 0.002 TYR E 233 PHE 0.020 0.002 PHE H 90 HIS 0.006 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.23 (31576) covalent geometry : angle 0.83900 / 0.42 (42888) hydrogen bonds : bond 0.04242 / 2.80 ( 832) hydrogen bonds : angle 5.76994 / 3.98 ( 2376) Misc. bond : bond 0.00032 / 0.02 ( 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 1342 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 298 poor density : 1044 time to evaluate : 1.092 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: 0.8629 (m-80) cc_final: 0.8341 (m-10) REVERT: A 128 ARG cc_start: 0.8863 (mmt90) cc_final: 0.8572 (mmt90) REVERT: A 165 PHE cc_start: 0.8162 (p90) cc_final: 0.7885 (p90) REVERT: A 202 GLN cc_start: 0.9316 (mt0) cc_final: 0.8816 (mt0) REVERT: A 206 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8027 (ttpt) REVERT: A 250 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7935 (pp) REVERT: A 254 GLU cc_start: 0.9402 (pp20) cc_final: 0.9105 (pm20) REVERT: A 258 TYR cc_start: 0.8738 (t80) cc_final: 0.8530 (t80) REVERT: A 285 ASN cc_start: 0.9470 (m110) cc_final: 0.9156 (m110) REVERT: A 297 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8856 (tm) REVERT: A 311 LYS cc_start: 0.8803 (tmtt) cc_final: 0.7939 (tppt) REVERT: A 337 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7292 (tt) REVERT: A 348 TYR cc_start: 0.9192 (t80) cc_final: 0.8839 (t80) REVERT: A 379 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9244 (tm) REVERT: A 386 MET cc_start: 0.9103 (ppp) cc_final: 0.8225 (ppp) REVERT: A 470 ASP cc_start: 0.8614 (m-30) cc_final: 0.8309 (m-30) REVERT: A 482 MET cc_start: 0.8704 (tpt) cc_final: 0.8447 (tpt) REVERT: A 487 GLU cc_start: 0.8404 (pm20) cc_final: 0.7946 (pm20) REVERT: A 488 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8232 (tm) REVERT: A 490 PHE cc_start: 0.8379 (m-80) cc_final: 0.8098 (m-80) REVERT: A 510 GLU cc_start: 0.6863 (mm-30) cc_final: 0.6511 (mm-30) REVERT: B 65 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9041 (pt) REVERT: B 165 PHE cc_start: 0.8013 (p90) cc_final: 0.7775 (p90) REVERT: B 176 GLU cc_start: 0.9171 (mp0) cc_final: 0.8872 (mp0) REVERT: B 199 GLU cc_start: 0.9309 (tp30) cc_final: 0.8968 (tp30) REVERT: B 202 GLN cc_start: 0.9297 (mt0) cc_final: 0.8939 (mt0) REVERT: B 206 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8154 (ttpt) REVERT: B 216 ASP cc_start: 0.9028 (t70) cc_final: 0.8652 (t0) REVERT: B 250 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7804 (pp) REVERT: B 283 GLN cc_start: 0.8738 (tt0) cc_final: 0.8506 (mt0) REVERT: B 311 LYS cc_start: 0.8948 (tmtt) cc_final: 0.8436 (tptt) REVERT: B 337 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7233 (tt) REVERT: B 385 MET cc_start: 0.8638 (ttp) cc_final: 0.8418 (ttp) REVERT: B 386 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8245 (pmm) REVERT: B 407 ARG cc_start: 0.7384 (ttt180) cc_final: 0.7074 (ttt90) REVERT: B 420 MET cc_start: 0.6805 (mmm) cc_final: 0.6411 (mmm) REVERT: B 470 ASP cc_start: 0.8568 (m-30) cc_final: 0.8161 (m-30) REVERT: B 482 MET cc_start: 0.8644 (tpt) cc_final: 0.8308 (tpt) REVERT: B 487 GLU cc_start: 0.8604 (pm20) cc_final: 0.8270 (pm20) REVERT: B 490 PHE cc_start: 0.8375 (m-80) cc_final: 0.7884 (m-80) REVERT: B 509 TYR cc_start: 0.7816 (p90) cc_final: 0.7601 (p90) REVERT: C 32 TYR cc_start: 0.8652 (m-80) cc_final: 0.8419 (m-10) REVERT: C 73 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.6833 (t) REVERT: C 128 ARG cc_start: 0.8833 (mmt90) cc_final: 0.8549 (mmt90) REVERT: C 165 PHE cc_start: 0.8070 (p90) cc_final: 0.7863 (p90) REVERT: C 199 GLU cc_start: 0.9502 (tp30) cc_final: 0.9201 (tp30) REVERT: C 206 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8007 (ttpt) REVERT: C 208 LYS cc_start: 0.8653 (mtpp) cc_final: 0.8424 (ttmm) REVERT: C 216 ASP cc_start: 0.9096 (t70) cc_final: 0.8720 (t0) REVERT: C 235 LEU cc_start: 0.9178 (mt) cc_final: 0.8975 (mt) REVERT: C 250 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7783 (pp) REVERT: C 261 ASP cc_start: 0.8783 (m-30) cc_final: 0.8442 (p0) REVERT: C 265 GLN cc_start: 0.9311 (mm110) cc_final: 0.9075 (mm-40) REVERT: C 297 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8727 (tm) REVERT: C 311 LYS cc_start: 0.8807 (tmtt) cc_final: 0.7940 (tppt) REVERT: C 337 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7149 (tt) REVERT: C 386 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8056 (ppp) REVERT: C 420 MET cc_start: 0.6587 (mmm) cc_final: 0.6153 (mmm) REVERT: C 470 ASP cc_start: 0.8653 (m-30) cc_final: 0.8220 (m-30) REVERT: C 482 MET cc_start: 0.8711 (tpt) cc_final: 0.8490 (tpt) REVERT: C 487 GLU cc_start: 0.8568 (pm20) cc_final: 0.8140 (pm20) REVERT: C 488 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8122 (tm) REVERT: C 490 PHE cc_start: 0.8466 (m-80) cc_final: 0.8115 (m-80) REVERT: C 509 TYR cc_start: 0.7708 (p90) cc_final: 0.7405 (p90) REVERT: C 510 GLU cc_start: 0.6747 (mm-30) cc_final: 0.6369 (mm-30) REVERT: C 514 PHE cc_start: 0.7543 (p90) cc_final: 0.7289 (p90) REVERT: D 73 VAL cc_start: 0.8250 (OUTLIER) cc_final: 0.6725 (t) REVERT: D 78 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7912 (ttt) REVERT: D 128 ARG cc_start: 0.8833 (mmt90) cc_final: 0.8568 (ttm-80) REVERT: D 165 PHE cc_start: 0.8039 (p90) cc_final: 0.7784 (p90) REVERT: D 176 GLU cc_start: 0.9241 (mp0) cc_final: 0.8977 (mp0) REVERT: D 199 GLU cc_start: 0.9512 (tp30) cc_final: 0.9222 (tp30) REVERT: D 206 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8030 (ttpt) REVERT: D 216 ASP cc_start: 0.9070 (t70) cc_final: 0.8713 (t0) REVERT: D 297 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8904 (tm) REVERT: D 311 LYS cc_start: 0.8910 (tmtt) cc_final: 0.8387 (tptt) REVERT: D 337 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7315 (tt) REVERT: D 386 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8490 (pmm) REVERT: D 390 LEU cc_start: 0.9109 (tt) cc_final: 0.8593 (tt) REVERT: D 400 TYR cc_start: 0.7803 (m-80) cc_final: 0.7476 (m-80) REVERT: D 420 MET cc_start: 0.6727 (mmm) cc_final: 0.6322 (mmm) REVERT: D 470 ASP cc_start: 0.8700 (m-30) cc_final: 0.8326 (m-30) REVERT: D 482 MET cc_start: 0.8664 (tpt) cc_final: 0.8402 (tpt) REVERT: D 487 GLU cc_start: 0.8558 (pm20) cc_final: 0.8118 (pm20) REVERT: D 490 PHE cc_start: 0.8447 (m-80) cc_final: 0.8014 (m-80) REVERT: D 509 TYR cc_start: 0.7726 (p90) cc_final: 0.7500 (p90) REVERT: D 510 GLU cc_start: 0.6764 (mm-30) cc_final: 0.6528 (mm-30) REVERT: D 514 PHE cc_start: 0.7548 (p90) cc_final: 0.7211 (p90) REVERT: E 78 MET cc_start: 0.8496 (ttm) cc_final: 0.8122 (ttt) REVERT: E 128 ARG cc_start: 0.8789 (mmt90) cc_final: 0.8514 (mmt90) REVERT: E 165 PHE cc_start: 0.8164 (p90) cc_final: 0.7654 (p90) REVERT: E 176 GLU cc_start: 0.9240 (mp0) cc_final: 0.8977 (mp0) REVERT: E 185 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7553 (mt) REVERT: E 206 LYS cc_start: 0.8209 (tppt) cc_final: 0.7772 (tppt) REVERT: E 216 ASP cc_start: 0.9100 (t70) cc_final: 0.8740 (t0) REVERT: E 235 LEU cc_start: 0.9183 (mt) cc_final: 0.8973 (mt) REVERT: E 250 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7755 (pp) REVERT: E 258 TYR cc_start: 0.8636 (t80) cc_final: 0.8289 (t80) REVERT: E 261 ASP cc_start: 0.8867 (m-30) cc_final: 0.8573 (p0) REVERT: E 265 GLN cc_start: 0.9358 (mm110) cc_final: 0.9136 (mm-40) REVERT: E 297 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8825 (tm) REVERT: E 311 LYS cc_start: 0.8877 (tmtt) cc_final: 0.8423 (tptt) REVERT: E 337 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7173 (tt) REVERT: E 385 MET cc_start: 0.8436 (ttp) cc_final: 0.8060 (ttp) REVERT: E 386 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8098 (ppp) REVERT: E 420 MET cc_start: 0.6731 (mmm) cc_final: 0.6330 (mmm) REVERT: E 470 ASP cc_start: 0.8749 (m-30) cc_final: 0.8287 (m-30) REVERT: E 482 MET cc_start: 0.8649 (tpt) cc_final: 0.8416 (tpt) REVERT: E 487 GLU cc_start: 0.8626 (pm20) cc_final: 0.8186 (pm20) REVERT: E 490 PHE cc_start: 0.8426 (m-80) cc_final: 0.7978 (m-80) REVERT: E 509 TYR cc_start: 0.7830 (p90) cc_final: 0.7447 (p90) REVERT: E 510 GLU cc_start: 0.6791 (mm-30) cc_final: 0.6371 (mm-30) REVERT: F 62 LYS cc_start: 0.9295 (mmtp) cc_final: 0.8831 (mttm) REVERT: F 78 MET cc_start: 0.8551 (ttm) cc_final: 0.8173 (ttt) REVERT: F 165 PHE cc_start: 0.8246 (p90) cc_final: 0.7634 (p90) REVERT: F 176 GLU cc_start: 0.9219 (mp0) cc_final: 0.8944 (mp0) REVERT: F 199 GLU cc_start: 0.9523 (tp30) cc_final: 0.9166 (tp30) REVERT: F 206 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8091 (ttpt) REVERT: F 216 ASP cc_start: 0.9078 (t70) cc_final: 0.8738 (t0) REVERT: F 235 LEU cc_start: 0.9160 (mt) cc_final: 0.8536 (mt) REVERT: F 265 GLN cc_start: 0.9319 (mm110) cc_final: 0.9064 (mm-40) REVERT: F 297 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8900 (tm) REVERT: F 311 LYS cc_start: 0.8889 (tmtt) cc_final: 0.8409 (tptt) REVERT: F 337 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7191 (tt) REVERT: F 379 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9176 (tm) REVERT: F 386 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8255 (ppp) REVERT: F 470 ASP cc_start: 0.8707 (m-30) cc_final: 0.8274 (m-30) REVERT: F 482 MET cc_start: 0.8661 (tpt) cc_final: 0.8341 (tpt) REVERT: F 487 GLU cc_start: 0.8704 (pm20) cc_final: 0.8372 (pm20) REVERT: F 490 PHE cc_start: 0.8456 (m-80) cc_final: 0.7942 (m-80) REVERT: F 509 TYR cc_start: 0.7840 (p90) cc_final: 0.7620 (p90) REVERT: F 514 PHE cc_start: 0.7579 (p90) cc_final: 0.7248 (p90) REVERT: G 32 TYR cc_start: 0.8630 (m-80) cc_final: 0.8404 (m-10) REVERT: G 165 PHE cc_start: 0.8094 (p90) cc_final: 0.7842 (p90) REVERT: G 199 GLU cc_start: 0.9510 (tp30) cc_final: 0.9108 (tp30) REVERT: G 203 ARG cc_start: 0.9365 (ptp-110) cc_final: 0.9042 (ptp-110) REVERT: G 206 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8083 (ttpt) REVERT: G 250 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7932 (pp) REVERT: G 258 TYR cc_start: 0.8639 (t80) cc_final: 0.8406 (t80) REVERT: G 297 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8897 (tm) REVERT: G 311 LYS cc_start: 0.8901 (tmtt) cc_final: 0.8075 (tppt) REVERT: G 337 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7201 (tt) REVERT: G 379 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9329 (tm) REVERT: G 385 MET cc_start: 0.8465 (ttp) cc_final: 0.8021 (ttp) REVERT: G 386 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8152 (ppp) REVERT: G 400 TYR cc_start: 0.7597 (m-80) cc_final: 0.7389 (m-80) REVERT: G 407 ARG cc_start: 0.7373 (ttt180) cc_final: 0.6810 (ttt90) REVERT: G 420 MET cc_start: 0.6750 (mmm) cc_final: 0.6371 (mmm) REVERT: G 470 ASP cc_start: 0.8617 (m-30) cc_final: 0.8368 (m-30) REVERT: G 482 MET cc_start: 0.8699 (tpt) cc_final: 0.8356 (tpt) REVERT: G 484 TYR cc_start: 0.9071 (m-10) cc_final: 0.8867 (m-10) REVERT: G 487 GLU cc_start: 0.8680 (pm20) cc_final: 0.8355 (pm20) REVERT: G 490 PHE cc_start: 0.8435 (m-80) cc_final: 0.8075 (m-80) REVERT: G 510 GLU cc_start: 0.6834 (mm-30) cc_final: 0.6375 (mm-30) REVERT: G 514 PHE cc_start: 0.7563 (p90) cc_final: 0.7321 (p90) REVERT: H 32 TYR cc_start: 0.8395 (m-10) cc_final: 0.8081 (m-10) REVERT: H 62 LYS cc_start: 0.9320 (mmtp) cc_final: 0.8853 (mttm) REVERT: H 65 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9062 (pt) REVERT: H 66 VAL cc_start: 0.8924 (OUTLIER) cc_final: 0.8577 (p) REVERT: H 73 VAL cc_start: 0.8440 (OUTLIER) cc_final: 0.7155 (t) REVERT: H 136 ARG cc_start: 0.9016 (ptp-110) cc_final: 0.8732 (ptp90) REVERT: H 161 ARG cc_start: 0.9617 (mpp-170) cc_final: 0.9378 (mpp80) REVERT: H 165 PHE cc_start: 0.8128 (p90) cc_final: 0.7836 (p90) REVERT: H 199 GLU cc_start: 0.9504 (tp30) cc_final: 0.9248 (tp30) REVERT: H 206 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8000 (ttpt) REVERT: H 216 ASP cc_start: 0.8967 (t70) cc_final: 0.8632 (t0) REVERT: H 235 LEU cc_start: 0.9165 (mt) cc_final: 0.8577 (mt) REVERT: H 250 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.7925 (pp) REVERT: H 297 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8884 (tm) REVERT: H 311 LYS cc_start: 0.8872 (tmtt) cc_final: 0.8378 (tptt) REVERT: H 337 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7357 (tt) REVERT: H 386 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8130 (pmm) REVERT: H 400 TYR cc_start: 0.7847 (m-80) cc_final: 0.7194 (m-80) REVERT: H 401 PHE cc_start: 0.8245 (p90) cc_final: 0.7923 (p90) REVERT: H 470 ASP cc_start: 0.8746 (m-30) cc_final: 0.8387 (m-30) REVERT: H 482 MET cc_start: 0.8616 (tpt) cc_final: 0.8349 (tpt) REVERT: H 487 GLU cc_start: 0.8564 (pm20) cc_final: 0.8130 (pm20) REVERT: H 490 PHE cc_start: 0.8369 (m-80) cc_final: 0.7922 (m-80) REVERT: H 509 TYR cc_start: 0.7994 (p90) cc_final: 0.7776 (p90) REVERT: H 514 PHE cc_start: 0.7617 (p90) cc_final: 0.7257 (p90) outliers start: 298 outliers final: 178 residues processed: 1182 average time/residue: 0.1868 time to fit residues: 356.7316 Evaluate side-chains 1178 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 226 poor density : 952 time to evaluate : 1.506 ------------------------------------------------------------------------------- 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 65 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 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 238 LYS 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 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 488 LEU Chi-restraints excluded: chain A residue 498 GLN 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 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 222 ILE Chi-restraints excluded: chain B residue 238 LYS 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 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 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 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 65 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 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 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 C residue 488 LEU 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 65 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 314 ILE 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 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 E residue 488 LEU 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 72 THR 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 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 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 157 ILE Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 238 LYS 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 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 238 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 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 351 SER Chi-restraints excluded: chain H residue 355 ARG Chi-restraints excluded: chain H residue 362 ILE 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: 1.9990 chunk 100 optimal weight: 8.9990 chunk 237 optimal weight: 4.9990 chunk 185 optimal weight: 6.9990 chunk 323 optimal weight: 1.9990 chunk 304 optimal weight: 5.9990 chunk 282 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN 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 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 GLN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN ** C 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 GLN C 498 GLN ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 GLN E 498 GLN ** F 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 GLN F 309 GLN F 312 ASN ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 283 GLN H 465 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.161468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.123889 restraints weight = 51082.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.129224 restraints weight = 30021.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.132930 restraints weight = 20690.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.135580 restraints weight = 15724.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.137593 restraints weight = 12735.038| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 31592 Z= 0.172 Angle : 0.810 13.449 42888 Z= 0.392 Chirality : 0.049 0.189 4888 Planarity : 0.005 0.084 5328 Dihedral : 16.820 151.855 4715 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 9.34 % Allowed : 26.47 % Favored : 64.19 % 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: -2.41 (0.13), residues: 3880 helix: -1.65 (0.13), residues: 1296 sheet: -2.53 (0.21), residues: 472 loop : -1.25 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 182 TYR 0.033 0.002 TYR A 233 PHE 0.017 0.001 PHE H 90 HIS 0.006 0.001 HIS C 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (31576) covalent geometry : angle 0.81020 / 0.39 (42888) hydrogen bonds : bond 0.03751 / 2.45 ( 832) hydrogen bonds : angle 5.55331 / 3.85 ( 2376) Misc. bond : bond 0.00034 / 0.02 ( 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 1348 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 298 poor density : 1050 time to evaluate : 1.273 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: 0.8545 (m-80) cc_final: 0.8322 (m-10) REVERT: A 51 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8031 (pp) REVERT: A 128 ARG cc_start: 0.8842 (mmt90) cc_final: 0.8559 (mmt90) REVERT: A 165 PHE cc_start: 0.8085 (p90) cc_final: 0.7856 (p90) REVERT: A 206 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7972 (ttpt) REVERT: A 208 LYS cc_start: 0.8295 (ttmm) cc_final: 0.8042 (mtpp) REVERT: A 230 ASN cc_start: 0.8679 (t0) cc_final: 0.8242 (t0) REVERT: A 250 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7884 (pp) REVERT: A 254 GLU cc_start: 0.9325 (pp20) cc_final: 0.9093 (pm20) REVERT: A 285 ASN cc_start: 0.9463 (m110) cc_final: 0.9160 (m110) REVERT: A 297 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8825 (tm) REVERT: A 311 LYS cc_start: 0.8767 (tmtt) cc_final: 0.7892 (tppt) REVERT: A 337 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7148 (tt) REVERT: A 348 TYR cc_start: 0.9176 (t80) cc_final: 0.8844 (t80) REVERT: A 379 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9252 (tm) REVERT: A 386 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8243 (ppp) REVERT: A 470 ASP cc_start: 0.8656 (m-30) cc_final: 0.8279 (m-30) REVERT: A 482 MET cc_start: 0.8662 (tpt) cc_final: 0.8371 (tpt) REVERT: A 484 TYR cc_start: 0.9156 (m-10) cc_final: 0.8953 (m-80) REVERT: A 487 GLU cc_start: 0.8404 (pm20) cc_final: 0.8011 (pm20) REVERT: A 490 PHE cc_start: 0.8303 (m-80) cc_final: 0.8005 (m-80) REVERT: A 509 TYR cc_start: 0.7710 (p90) cc_final: 0.7224 (p90) REVERT: A 510 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6790 (mm-30) REVERT: B 109 LYS cc_start: 0.8705 (mmtm) cc_final: 0.8393 (mptt) REVERT: B 128 ARG cc_start: 0.9131 (mmm-85) cc_final: 0.8812 (mmt90) REVERT: B 165 PHE cc_start: 0.7942 (p90) cc_final: 0.7709 (p90) REVERT: B 199 GLU cc_start: 0.9450 (tp30) cc_final: 0.9210 (tp30) REVERT: B 206 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8194 (ttpt) REVERT: B 216 ASP cc_start: 0.8991 (t70) cc_final: 0.8621 (t0) REVERT: B 261 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8371 (p0) REVERT: B 309 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8800 (pt0) REVERT: B 311 LYS cc_start: 0.8913 (tmtt) cc_final: 0.8384 (tptt) REVERT: B 337 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7122 (tt) REVERT: B 385 MET cc_start: 0.8484 (ttp) cc_final: 0.8228 (ttp) REVERT: B 386 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8326 (pmm) REVERT: B 407 ARG cc_start: 0.7471 (ttt180) cc_final: 0.7189 (ttt90) REVERT: B 420 MET cc_start: 0.6858 (mmm) cc_final: 0.6445 (mmm) REVERT: B 470 ASP cc_start: 0.8694 (m-30) cc_final: 0.8310 (m-30) REVERT: B 482 MET cc_start: 0.8623 (tpt) cc_final: 0.8290 (tpt) REVERT: B 487 GLU cc_start: 0.8540 (pm20) cc_final: 0.8289 (pm20) REVERT: B 490 PHE cc_start: 0.8358 (m-80) cc_final: 0.7898 (m-80) REVERT: B 509 TYR cc_start: 0.7808 (p90) cc_final: 0.7559 (p90) REVERT: B 510 GLU cc_start: 0.6652 (mm-30) cc_final: 0.6221 (mm-30) REVERT: C 32 TYR cc_start: 0.8569 (m-80) cc_final: 0.8336 (m-10) REVERT: C 109 LYS cc_start: 0.8746 (mmtm) cc_final: 0.8429 (mptt) REVERT: C 165 PHE cc_start: 0.8064 (p90) cc_final: 0.7852 (p90) REVERT: C 199 GLU cc_start: 0.9479 (tp30) cc_final: 0.9223 (tp30) REVERT: C 203 ARG cc_start: 0.9359 (ptp-110) cc_final: 0.9156 (ptp-110) REVERT: C 206 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8087 (ttpt) REVERT: C 208 LYS cc_start: 0.8705 (mtpp) cc_final: 0.8036 (mtpp) REVERT: C 214 GLU cc_start: 0.9284 (mm-30) cc_final: 0.9074 (mp0) REVERT: C 216 ASP cc_start: 0.9082 (t70) cc_final: 0.8709 (t0) REVERT: C 235 LEU cc_start: 0.9075 (mt) cc_final: 0.8862 (mt) REVERT: C 250 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7734 (pp) REVERT: C 258 TYR cc_start: 0.8526 (t80) cc_final: 0.8159 (t80) REVERT: C 297 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8828 (tm) REVERT: C 311 LYS cc_start: 0.8766 (tmtt) cc_final: 0.7941 (tppt) REVERT: C 337 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7206 (tt) REVERT: C 355 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8534 (ttm110) REVERT: C 386 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8368 (ppp) REVERT: C 400 TYR cc_start: 0.7534 (m-80) cc_final: 0.7210 (m-80) REVERT: C 407 ARG cc_start: 0.7268 (ttt180) cc_final: 0.6942 (ttt90) REVERT: C 420 MET cc_start: 0.6671 (mmm) cc_final: 0.6218 (mmm) REVERT: C 470 ASP cc_start: 0.8642 (m-30) cc_final: 0.8357 (m-30) REVERT: C 482 MET cc_start: 0.8667 (tpt) cc_final: 0.8428 (tpt) REVERT: C 484 TYR cc_start: 0.8907 (m-10) cc_final: 0.8635 (m-10) REVERT: C 487 GLU cc_start: 0.8454 (pm20) cc_final: 0.8034 (pm20) REVERT: C 488 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8064 (tm) REVERT: C 490 PHE cc_start: 0.8377 (m-80) cc_final: 0.8094 (m-80) REVERT: C 509 TYR cc_start: 0.7740 (p90) cc_final: 0.7487 (p90) REVERT: C 510 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6647 (mm-30) REVERT: C 514 PHE cc_start: 0.7423 (p90) cc_final: 0.7107 (p90) REVERT: D 73 VAL cc_start: 0.8202 (OUTLIER) cc_final: 0.6692 (t) REVERT: D 165 PHE cc_start: 0.7934 (p90) cc_final: 0.7712 (p90) REVERT: D 199 GLU cc_start: 0.9453 (tp30) cc_final: 0.9245 (tp30) REVERT: D 206 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8096 (ttpt) REVERT: D 216 ASP cc_start: 0.9064 (t70) cc_final: 0.8709 (t0) REVERT: D 297 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8900 (tm) REVERT: D 309 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8838 (pt0) REVERT: D 311 LYS cc_start: 0.8847 (tmtt) cc_final: 0.7933 (tppt) REVERT: D 337 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7221 (tt) REVERT: D 352 GLU cc_start: 0.8769 (tp30) cc_final: 0.8423 (tp30) REVERT: D 386 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8284 (pmm) REVERT: D 390 LEU cc_start: 0.9026 (tt) cc_final: 0.8480 (tt) REVERT: D 400 TYR cc_start: 0.7792 (m-80) cc_final: 0.7416 (m-80) REVERT: D 407 ARG cc_start: 0.7280 (ttt180) cc_final: 0.6647 (ttt180) REVERT: D 420 MET cc_start: 0.6750 (mmm) cc_final: 0.6330 (mmm) REVERT: D 470 ASP cc_start: 0.8763 (m-30) cc_final: 0.8364 (m-30) REVERT: D 482 MET cc_start: 0.8622 (tpt) cc_final: 0.8354 (tpt) REVERT: D 487 GLU cc_start: 0.8534 (pm20) cc_final: 0.8175 (pm20) REVERT: D 490 PHE cc_start: 0.8311 (m-80) cc_final: 0.7912 (m-80) REVERT: D 509 TYR cc_start: 0.7822 (p90) cc_final: 0.7593 (p90) REVERT: D 510 GLU cc_start: 0.6815 (mm-30) cc_final: 0.6322 (mm-30) REVERT: E 65 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8963 (pt) REVERT: E 78 MET cc_start: 0.8263 (ttm) cc_final: 0.7919 (ttt) REVERT: E 109 LYS cc_start: 0.8804 (mmtm) cc_final: 0.8396 (mptt) REVERT: E 128 ARG cc_start: 0.8794 (mmt90) cc_final: 0.8504 (mmt90) REVERT: E 165 PHE cc_start: 0.8115 (p90) cc_final: 0.7867 (p90) REVERT: E 185 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7495 (mt) REVERT: E 206 LYS cc_start: 0.8192 (tppt) cc_final: 0.7867 (tppt) REVERT: E 216 ASP cc_start: 0.9110 (t70) cc_final: 0.8757 (t0) REVERT: E 235 LEU cc_start: 0.9092 (mt) cc_final: 0.8867 (mt) REVERT: E 250 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7719 (pp) REVERT: E 297 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8801 (tm) REVERT: E 311 LYS cc_start: 0.8850 (tmtt) cc_final: 0.7982 (tppt) REVERT: E 337 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7181 (tt) REVERT: E 348 TYR cc_start: 0.9269 (t80) cc_final: 0.8875 (t80) REVERT: E 385 MET cc_start: 0.8445 (ttp) cc_final: 0.8221 (ttp) REVERT: E 386 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8333 (ppp) REVERT: E 420 MET cc_start: 0.6730 (mmm) cc_final: 0.6336 (mmm) REVERT: E 470 ASP cc_start: 0.8700 (m-30) cc_final: 0.8427 (m-30) REVERT: E 482 MET cc_start: 0.8613 (tpt) cc_final: 0.8384 (tpt) REVERT: E 487 GLU cc_start: 0.8572 (pm20) cc_final: 0.8219 (pm20) REVERT: E 489 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8060 (tttt) REVERT: E 490 PHE cc_start: 0.8399 (m-80) cc_final: 0.8092 (m-80) REVERT: E 509 TYR cc_start: 0.7912 (p90) cc_final: 0.7642 (p90) REVERT: E 510 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6661 (mm-30) REVERT: F 62 LYS cc_start: 0.9262 (mmtp) cc_final: 0.8767 (mttm) REVERT: F 78 MET cc_start: 0.8432 (ttm) cc_final: 0.8022 (ttt) REVERT: F 132 GLU cc_start: 0.9489 (mp0) cc_final: 0.9258 (mp0) REVERT: F 165 PHE cc_start: 0.8240 (p90) cc_final: 0.7967 (p90) REVERT: F 199 GLU cc_start: 0.9483 (tp30) cc_final: 0.9254 (tp30) REVERT: F 206 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8153 (ttpt) REVERT: F 216 ASP cc_start: 0.9069 (t70) cc_final: 0.8710 (t0) REVERT: F 235 LEU cc_start: 0.9072 (mt) cc_final: 0.8425 (mt) REVERT: F 261 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8300 (p0) REVERT: F 297 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8846 (tm) REVERT: F 309 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8901 (pt0) REVERT: F 311 LYS cc_start: 0.8895 (tmtt) cc_final: 0.8370 (tptt) REVERT: F 337 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7273 (tt) REVERT: F 386 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8219 (pmm) REVERT: F 399 GLU cc_start: 0.8800 (pm20) cc_final: 0.8165 (tt0) REVERT: F 407 ARG cc_start: 0.7609 (ttt180) cc_final: 0.6912 (ttt180) REVERT: F 470 ASP cc_start: 0.8786 (m-30) cc_final: 0.8436 (m-30) REVERT: F 482 MET cc_start: 0.8725 (tpt) cc_final: 0.8419 (tpt) REVERT: F 487 GLU cc_start: 0.8643 (pm20) cc_final: 0.8360 (pm20) REVERT: F 490 PHE cc_start: 0.8360 (m-80) cc_final: 0.7978 (m-80) REVERT: F 514 PHE cc_start: 0.7470 (p90) cc_final: 0.7094 (p90) REVERT: G 32 TYR cc_start: 0.8586 (m-80) cc_final: 0.8329 (m-10) REVERT: G 65 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9065 (pt) REVERT: G 109 LYS cc_start: 0.8822 (mmtm) cc_final: 0.8452 (mptt) REVERT: G 165 PHE cc_start: 0.8061 (p90) cc_final: 0.7771 (p90) REVERT: G 199 GLU cc_start: 0.9472 (tp30) cc_final: 0.9162 (tp30) REVERT: G 203 ARG cc_start: 0.9386 (ptp-110) cc_final: 0.9092 (ptp-110) REVERT: G 206 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8028 (ttpt) REVERT: G 208 LYS cc_start: 0.8155 (ttmm) cc_final: 0.7827 (ttmm) REVERT: G 297 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8847 (tm) REVERT: G 311 LYS cc_start: 0.8831 (tmtt) cc_final: 0.8037 (tppt) REVERT: G 337 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7236 (tt) REVERT: G 355 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8441 (ttm110) REVERT: G 379 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9293 (tm) REVERT: G 386 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8465 (pmm) REVERT: G 400 TYR cc_start: 0.7561 (m-80) cc_final: 0.7229 (m-80) REVERT: G 407 ARG cc_start: 0.7405 (ttt180) cc_final: 0.6862 (ttt90) REVERT: G 470 ASP cc_start: 0.8720 (m-30) cc_final: 0.8337 (m-30) REVERT: G 482 MET cc_start: 0.8689 (tpt) cc_final: 0.8452 (tpt) REVERT: G 484 TYR cc_start: 0.8904 (m-10) cc_final: 0.8543 (m-10) REVERT: G 487 GLU cc_start: 0.8634 (pm20) cc_final: 0.8269 (pm20) REVERT: G 488 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8032 (tm) REVERT: G 490 PHE cc_start: 0.8417 (m-80) cc_final: 0.8085 (m-80) REVERT: G 509 TYR cc_start: 0.7852 (p90) cc_final: 0.7437 (p90) REVERT: G 510 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6862 (mm-30) REVERT: H 62 LYS cc_start: 0.9274 (mmtp) cc_final: 0.8764 (mttm) REVERT: H 78 MET cc_start: 0.7794 (ttt) cc_final: 0.7415 (ttt) REVERT: H 109 LYS cc_start: 0.8752 (mmtm) cc_final: 0.8344 (mptt) REVERT: H 161 ARG cc_start: 0.9597 (mpp-170) cc_final: 0.9163 (mpt-90) REVERT: H 165 PHE cc_start: 0.8044 (p90) cc_final: 0.7799 (p90) REVERT: H 199 GLU cc_start: 0.9481 (tp30) cc_final: 0.9240 (tp30) REVERT: H 206 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8066 (ttpt) REVERT: H 216 ASP cc_start: 0.8960 (t70) cc_final: 0.8605 (t0) REVERT: H 235 LEU cc_start: 0.9126 (mt) cc_final: 0.8446 (mt) REVERT: H 283 GLN cc_start: 0.8768 (tt0) cc_final: 0.8494 (mt0) REVERT: H 297 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8853 (tm) REVERT: H 311 LYS cc_start: 0.8854 (tmtt) cc_final: 0.8352 (tptt) REVERT: H 337 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7276 (tt) REVERT: H 386 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8093 (pmm) REVERT: H 470 ASP cc_start: 0.8767 (m-30) cc_final: 0.8418 (m-30) REVERT: H 482 MET cc_start: 0.8611 (tpt) cc_final: 0.8359 (tpt) REVERT: H 487 GLU cc_start: 0.8571 (pm20) cc_final: 0.8187 (pm20) REVERT: H 490 PHE cc_start: 0.8327 (m-80) cc_final: 0.7854 (m-80) outliers start: 298 outliers final: 186 residues processed: 1184 average time/residue: 0.1886 time to fit residues: 358.1334 Evaluate side-chains 1197 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 959 time to evaluate : 1.189 ------------------------------------------------------------------------------- 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 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 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 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 362 ILE 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 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 115 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 238 LYS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 268 VAL 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 309 GLN 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 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 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 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 355 ARG Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 362 ILE 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 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 59 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 206 LYS 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 306 THR Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 361 VAL 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 408 LEU 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 222 ILE 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 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 351 SER Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 370 VAL 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 453 ILE Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 489 LYS 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 238 LYS Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 261 ASP 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 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 361 VAL 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 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 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 235 LEU Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 271 VAL 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 355 ARG Chi-restraints excluded: chain G residue 362 ILE 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 498 GLN 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 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 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 336 VAL Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 355 ARG Chi-restraints excluded: chain H residue 361 VAL 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 469 GLN Chi-restraints excluded: chain H residue 494 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.8714 > 50: distance: 95 - 98: 9.862 distance: 98 - 99: 7.169 distance: 99 - 100: 9.206 distance: 99 - 102: 7.537 distance: 100 - 101: 17.578 distance: 100 - 104: 5.382 distance: 102 - 103: 8.619 distance: 105 - 106: 4.900 distance: 106 - 107: 11.450 distance: 106 - 108: 11.293 distance: 109 - 110: 12.626 distance: 109 - 112: 6.597 distance: 110 - 111: 14.114 distance: 110 - 119: 3.693 distance: 112 - 113: 20.705 distance: 113 - 114: 6.511 distance: 114 - 115: 7.118 distance: 116 - 117: 4.813 distance: 116 - 118: 3.360 distance: 119 - 120: 7.584 distance: 119 - 125: 16.361 distance: 120 - 121: 10.354 distance: 120 - 123: 21.926 distance: 121 - 122: 15.425 distance: 121 - 126: 28.128 distance: 123 - 124: 7.867 distance: 124 - 125: 16.224 distance: 126 - 127: 16.281 distance: 127 - 128: 13.031 distance: 127 - 130: 10.452 distance: 128 - 129: 22.764 distance: 128 - 135: 4.602 distance: 129 - 152: 16.075 distance: 130 - 131: 23.818 distance: 131 - 132: 15.390 distance: 132 - 133: 12.739 distance: 132 - 134: 18.355 distance: 135 - 136: 9.659 distance: 136 - 137: 5.928 distance: 136 - 139: 4.250 distance: 137 - 138: 4.383 distance: 137 - 140: 8.944 distance: 138 - 159: 10.293 distance: 140 - 141: 10.972 distance: 141 - 142: 8.142 distance: 141 - 144: 4.758 distance: 142 - 143: 6.237 distance: 142 - 147: 12.785 distance: 143 - 171: 10.174 distance: 144 - 145: 17.456 distance: 144 - 146: 7.744 distance: 147 - 148: 8.159 distance: 148 - 149: 3.897 distance: 148 - 151: 3.652 distance: 149 - 150: 6.634 distance: 149 - 152: 3.734 distance: 150 - 179: 10.770 distance: 153 - 156: 3.819 distance: 155 - 185: 6.202 distance: 156 - 157: 3.475 distance: 156 - 158: 6.516 distance: 161 - 162: 3.243 distance: 162 - 191: 4.576 distance: 165 - 167: 3.231