Starting phenix.real_space_refine on Mon Sep 14 15:45:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uaj_20707/09_2026/6uaj_20707.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uaj_20707/09_2026/6uaj_20707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6uaj_20707/09_2026/6uaj_20707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uaj_20707/09_2026/6uaj_20707.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uaj_20707/09_2026/6uaj_20707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uaj_20707/09_2026/6uaj_20707.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6uaj_20707/09_2026/6uaj_20707.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uaj_20707/09_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Time building chain proxies: 6.18, per 1000 atoms: 0.20 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: 2.71 Conformation dependent library (CDL) restraints added in 1.3 seconds 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7104 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 48 sheets defined 34.4% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 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: 6.48 Time building geometry restraints manager: 3.58 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: 41447 4.11 - 8.22: 1101 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: 17932 34.54 - 69.09: 688 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=" O5' GTP H 602 " pdb=" O3A GTP H 602 " pdb=" PA GTP H 602 " pdb=" PB GTP H 602 " ideal model delta sinusoidal sigma weight residual -85.88 86.85 -172.72 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O5' GTP C 602 " pdb=" O3A GTP C 602 " pdb=" PA GTP C 602 " pdb=" PB GTP C 602 " ideal model delta sinusoidal sigma weight residual -85.88 86.83 -172.71 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O5' GTP A 602 " pdb=" O3A GTP A 602 " pdb=" PA GTP A 602 " pdb=" PB GTP A 602 " ideal model delta sinusoidal sigma weight residual -85.88 86.82 -172.70 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 18717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 4428 0.130 - 0.260: 396 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: 0.11 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 28.270 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.070 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.180 ------------------------------------------------------------------------------- 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 : 1.871 20.561 42888 Z= 1.025 Chirality : 0.086 0.650 4888 Planarity : 0.008 0.068 5328 Dihedral : 19.053 172.723 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 0.01810 / 1.00 (31576) covalent geometry : angle 1.87100 / 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 : 1.164 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: 0.1972 time to fit residues: 470.4304 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 : 1.114 ------------------------------------------------------------------------------- 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 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 309 GLN D 368 GLN ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN ** G 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN ** H 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 GLN H 368 GLN H 498 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.167064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.129261 restraints weight = 50389.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.134864 restraints weight = 28875.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.138736 restraints weight = 19591.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.141555 restraints weight = 14703.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.143549 restraints weight = 11779.450| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31592 Z= 0.167 Angle : 0.862 10.156 42888 Z= 0.419 Chirality : 0.050 0.170 4888 Planarity : 0.005 0.041 5328 Dihedral : 19.193 162.203 4954 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 7.71 % Allowed : 22.81 % 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: -3.11 (0.12), residues: 3880 helix: -2.15 (0.12), residues: 1224 sheet: -2.75 (0.18), residues: 520 loop : -1.78 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 149 TYR 0.023 0.002 TYR 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 0.00371 / 0.17 (31576) covalent geometry : angle 0.86183 / 0.42 (42888) hydrogen bonds : bond 0.05023 / 3.32 ( 832) hydrogen bonds : angle 6.04938 / 4.17 ( 2376) Misc. bond : bond 0.00064 / 0.04 ( 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 1327 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 246 poor density : 1081 time to evaluate : 1.071 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: 0.8645 (m-80) cc_final: 0.8347 (m-10) REVERT: A 73 VAL cc_start: 0.8296 (OUTLIER) cc_final: 0.6625 (t) REVERT: A 136 ARG cc_start: 0.8980 (ptp-110) cc_final: 0.8569 (ptp90) REVERT: A 202 GLN cc_start: 0.9289 (mt0) cc_final: 0.8891 (mt0) REVERT: A 206 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8014 (ttmm) REVERT: A 250 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7832 (pp) REVERT: A 254 GLU cc_start: 0.9307 (pp20) cc_final: 0.9094 (pm20) REVERT: A 285 ASN cc_start: 0.9455 (m110) cc_final: 0.9132 (m110) REVERT: A 297 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8694 (tm) REVERT: A 311 LYS cc_start: 0.8770 (tmtt) cc_final: 0.8319 (tptt) REVERT: A 352 GLU cc_start: 0.8570 (tp30) cc_final: 0.8365 (tp30) REVERT: A 386 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8363 (ppp) REVERT: A 407 ARG cc_start: 0.7438 (ttt180) cc_final: 0.7099 (ttt90) REVERT: A 420 MET cc_start: 0.6554 (mmm) cc_final: 0.6079 (mmm) REVERT: A 470 ASP cc_start: 0.8460 (m-30) cc_final: 0.8096 (m-30) REVERT: A 482 MET cc_start: 0.8456 (tpt) cc_final: 0.8100 (tpt) REVERT: A 487 GLU cc_start: 0.8517 (pm20) cc_final: 0.8031 (pm20) REVERT: A 490 PHE cc_start: 0.8251 (m-80) cc_final: 0.7860 (m-80) REVERT: A 509 TYR cc_start: 0.7800 (p90) cc_final: 0.7538 (p90) REVERT: A 514 PHE cc_start: 0.7108 (p90) cc_final: 0.6419 (p90) REVERT: B 161 ARG cc_start: 0.9518 (mpp-170) cc_final: 0.9054 (mtt90) REVERT: B 165 PHE cc_start: 0.7936 (p90) cc_final: 0.7672 (p90) REVERT: B 180 THR cc_start: 0.8160 (p) cc_final: 0.7804 (t) REVERT: B 199 GLU cc_start: 0.9292 (tp30) cc_final: 0.8769 (tp30) REVERT: B 202 GLN cc_start: 0.9322 (mt0) cc_final: 0.8968 (mt0) REVERT: B 203 ARG cc_start: 0.9010 (ptp-110) cc_final: 0.8790 (ptp-110) REVERT: B 206 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8169 (ttpt) REVERT: B 208 LYS cc_start: 0.8319 (mtpp) cc_final: 0.8090 (ttmm) REVERT: B 216 ASP cc_start: 0.8925 (t70) cc_final: 0.8589 (t0) REVERT: B 232 ASP cc_start: 0.9251 (t0) cc_final: 0.9021 (t0) REVERT: B 233 TYR cc_start: 0.9007 (m-80) cc_final: 0.8720 (m-80) REVERT: B 258 TYR cc_start: 0.8329 (t80) cc_final: 0.8048 (t80) REVERT: B 285 ASN cc_start: 0.9331 (m110) cc_final: 0.9087 (m110) REVERT: B 297 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8714 (tm) REVERT: B 311 LYS cc_start: 0.8918 (tmtt) cc_final: 0.8333 (tptt) REVERT: B 385 MET cc_start: 0.8554 (ttp) cc_final: 0.8263 (ttt) REVERT: B 386 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8299 (ppp) REVERT: B 399 GLU cc_start: 0.7231 (pp20) cc_final: 0.7023 (pp20) REVERT: B 400 TYR cc_start: 0.7895 (m-80) cc_final: 0.7430 (m-80) REVERT: B 401 PHE cc_start: 0.8256 (p90) cc_final: 0.8042 (p90) REVERT: B 482 MET cc_start: 0.8441 (tpt) cc_final: 0.8100 (tpt) REVERT: B 487 GLU cc_start: 0.8506 (pm20) cc_final: 0.8157 (pm20) REVERT: B 490 PHE cc_start: 0.8369 (m-80) cc_final: 0.7951 (m-80) REVERT: B 514 PHE cc_start: 0.7081 (p90) cc_final: 0.6848 (p90) REVERT: C 32 TYR cc_start: 0.8628 (m-80) cc_final: 0.8369 (m-10) REVERT: C 78 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.8020 (ttp) REVERT: C 199 GLU cc_start: 0.9303 (tp30) cc_final: 0.9009 (tp30) REVERT: C 202 GLN cc_start: 0.9329 (mt0) cc_final: 0.8932 (mt0) REVERT: C 206 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8114 (ttpt) REVERT: C 208 LYS cc_start: 0.8447 (mtpp) cc_final: 0.8213 (ttmm) REVERT: C 250 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7558 (pp) REVERT: C 261 ASP cc_start: 0.8848 (m-30) cc_final: 0.8627 (p0) REVERT: C 285 ASN cc_start: 0.9376 (m110) cc_final: 0.9050 (m110) REVERT: C 297 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8681 (tm) REVERT: C 311 LYS cc_start: 0.8845 (tmtt) cc_final: 0.8374 (tptt) REVERT: C 357 PHE cc_start: 0.8821 (m-80) cc_final: 0.8491 (m-10) REVERT: C 386 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8411 (ppp) REVERT: C 407 ARG cc_start: 0.7423 (ttt180) cc_final: 0.6834 (ttt90) REVERT: C 420 MET cc_start: 0.6424 (mmm) cc_final: 0.6006 (mmm) REVERT: C 466 HIS cc_start: 0.9015 (OUTLIER) cc_final: 0.8224 (t-90) REVERT: C 470 ASP cc_start: 0.8479 (m-30) cc_final: 0.8053 (m-30) REVERT: C 482 MET cc_start: 0.8496 (tpt) cc_final: 0.8160 (tpt) REVERT: C 487 GLU cc_start: 0.8561 (pm20) cc_final: 0.8204 (pm20) REVERT: C 490 PHE cc_start: 0.8267 (m-80) cc_final: 0.7922 (m-80) REVERT: C 514 PHE cc_start: 0.7144 (p90) cc_final: 0.6918 (p90) REVERT: D 73 VAL cc_start: 0.8170 (OUTLIER) cc_final: 0.6351 (t) REVERT: D 78 MET cc_start: 0.8337 (ttm) cc_final: 0.8015 (ttp) REVERT: D 94 ASN cc_start: 0.7681 (p0) cc_final: 0.7467 (p0) REVERT: D 161 ARG cc_start: 0.9550 (mpp-170) cc_final: 0.9182 (mpt-90) REVERT: D 165 PHE cc_start: 0.7992 (p90) cc_final: 0.7729 (p90) REVERT: D 180 THR cc_start: 0.8452 (p) cc_final: 0.8047 (t) REVERT: D 199 GLU cc_start: 0.9488 (tp30) cc_final: 0.9203 (tp30) REVERT: D 206 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8022 (ttpt) REVERT: D 216 ASP cc_start: 0.8955 (t70) cc_final: 0.8630 (t0) REVERT: D 233 TYR cc_start: 0.9019 (m-80) cc_final: 0.8737 (m-80) REVERT: D 273 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8474 (mm) REVERT: D 297 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8774 (tm) REVERT: D 311 LYS cc_start: 0.8913 (tmtt) cc_final: 0.8474 (tptt) REVERT: D 385 MET cc_start: 0.8603 (ttp) cc_final: 0.8274 (ttt) REVERT: D 386 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8321 (ppp) REVERT: D 407 ARG cc_start: 0.7482 (ttt180) cc_final: 0.7228 (ttt180) REVERT: D 461 ILE cc_start: 0.9131 (pp) cc_final: 0.8707 (pt) REVERT: D 482 MET cc_start: 0.8554 (tpt) cc_final: 0.8184 (tpt) REVERT: D 484 TYR cc_start: 0.9035 (m-10) cc_final: 0.8104 (m-10) REVERT: D 487 GLU cc_start: 0.8550 (pm20) cc_final: 0.8194 (pm20) REVERT: D 490 PHE cc_start: 0.8325 (m-80) cc_final: 0.7941 (m-80) REVERT: E 32 TYR cc_start: 0.8598 (m-10) cc_final: 0.8349 (m-10) REVERT: E 78 MET cc_start: 0.8437 (ttm) cc_final: 0.8214 (ttt) REVERT: E 165 PHE cc_start: 0.8113 (p90) cc_final: 0.7686 (p90) REVERT: E 185 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7564 (mt) REVERT: E 199 GLU cc_start: 0.9509 (tp30) cc_final: 0.9244 (tp30) REVERT: E 206 LYS cc_start: 0.7972 (tppt) cc_final: 0.7645 (tppt) REVERT: E 216 ASP cc_start: 0.8994 (t70) cc_final: 0.8646 (t0) REVERT: E 250 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7552 (pp) REVERT: E 285 ASN cc_start: 0.9329 (m110) cc_final: 0.9027 (m110) REVERT: E 297 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8723 (tm) REVERT: E 311 LYS cc_start: 0.8881 (tmtt) cc_final: 0.8445 (tptt) REVERT: E 385 MET cc_start: 0.8439 (ttp) cc_final: 0.8017 (ttp) REVERT: E 386 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8321 (ppp) REVERT: E 420 MET cc_start: 0.6501 (mmm) cc_final: 0.6125 (mmm) REVERT: E 466 HIS cc_start: 0.9115 (OUTLIER) cc_final: 0.8330 (t-90) REVERT: E 482 MET cc_start: 0.8471 (tpt) cc_final: 0.8148 (tpt) REVERT: E 487 GLU cc_start: 0.8578 (pm20) cc_final: 0.8226 (pm20) REVERT: E 490 PHE cc_start: 0.8377 (m-80) cc_final: 0.8032 (m-80) REVERT: F 78 MET cc_start: 0.8450 (ttm) cc_final: 0.8220 (ttt) REVERT: F 109 LYS cc_start: 0.8665 (mmtm) cc_final: 0.8406 (mmtm) REVERT: F 165 PHE cc_start: 0.8148 (p90) cc_final: 0.7629 (p90) REVERT: F 180 THR cc_start: 0.8223 (p) cc_final: 0.7887 (t) REVERT: F 199 GLU cc_start: 0.9497 (tp30) cc_final: 0.9231 (tp30) REVERT: F 206 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8093 (ttpt) REVERT: F 216 ASP cc_start: 0.8989 (t70) cc_final: 0.8654 (t0) REVERT: F 258 TYR cc_start: 0.8350 (t80) cc_final: 0.8019 (t80) REVERT: F 297 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8710 (tm) REVERT: F 311 LYS cc_start: 0.8880 (tmtt) cc_final: 0.8453 (tptt) REVERT: F 386 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8241 (ppp) REVERT: F 400 TYR cc_start: 0.7950 (m-80) cc_final: 0.7423 (m-80) REVERT: F 401 PHE cc_start: 0.8256 (p90) cc_final: 0.8004 (p90) REVERT: F 466 HIS cc_start: 0.9027 (OUTLIER) cc_final: 0.8278 (t-90) REVERT: F 482 MET cc_start: 0.8528 (tpt) cc_final: 0.8193 (tpt) REVERT: F 487 GLU cc_start: 0.8621 (pm20) cc_final: 0.8266 (pm20) REVERT: F 490 PHE cc_start: 0.8422 (m-80) cc_final: 0.8015 (m-80) REVERT: F 514 PHE cc_start: 0.7201 (p90) cc_final: 0.6944 (p90) REVERT: G 32 TYR cc_start: 0.8599 (m-80) cc_final: 0.8387 (m-10) REVERT: G 73 VAL cc_start: 0.8390 (OUTLIER) cc_final: 0.6751 (t) REVERT: G 109 LYS cc_start: 0.8770 (mmtm) cc_final: 0.8507 (mmtm) REVERT: G 165 PHE cc_start: 0.8067 (p90) cc_final: 0.7834 (p90) REVERT: G 179 MET cc_start: 0.7776 (ptm) cc_final: 0.7493 (ptt) REVERT: G 199 GLU cc_start: 0.9505 (tp30) cc_final: 0.9119 (tp30) REVERT: G 206 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7984 (ttpt) REVERT: G 285 ASN cc_start: 0.9387 (m110) cc_final: 0.9054 (m110) REVERT: G 297 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8730 (tm) REVERT: G 311 LYS cc_start: 0.8870 (tmtt) cc_final: 0.8440 (tptt) REVERT: G 385 MET cc_start: 0.8439 (ttp) cc_final: 0.7993 (ttp) REVERT: G 386 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8333 (ppp) REVERT: G 420 MET cc_start: 0.6511 (mmm) cc_final: 0.6153 (mmm) REVERT: G 441 GLN cc_start: 0.8405 (mm-40) cc_final: 0.8146 (mm-40) REVERT: G 466 HIS cc_start: 0.9054 (OUTLIER) cc_final: 0.8286 (t-90) REVERT: G 470 ASP cc_start: 0.8423 (m-30) cc_final: 0.8028 (m-30) REVERT: G 482 MET cc_start: 0.8515 (tpt) cc_final: 0.8178 (tpt) REVERT: G 487 GLU cc_start: 0.8612 (pm20) cc_final: 0.8267 (pm20) REVERT: G 490 PHE cc_start: 0.8379 (m-80) cc_final: 0.8047 (m-80) REVERT: H 32 TYR cc_start: 0.8532 (m-10) cc_final: 0.7930 (m-10) REVERT: H 136 ARG cc_start: 0.9007 (ptp-110) cc_final: 0.8678 (ptp90) REVERT: H 165 PHE cc_start: 0.8086 (p90) cc_final: 0.7602 (p90) REVERT: H 180 THR cc_start: 0.8205 (p) cc_final: 0.7930 (t) REVERT: H 199 GLU cc_start: 0.9479 (tp30) cc_final: 0.9225 (tp30) REVERT: H 206 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8107 (ttmm) REVERT: H 216 ASP cc_start: 0.8804 (t70) cc_final: 0.8451 (t0) REVERT: H 297 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8684 (tm) REVERT: H 311 LYS cc_start: 0.8833 (tmtt) cc_final: 0.8387 (tptt) REVERT: H 386 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8411 (ppp) REVERT: H 390 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8886 (tt) REVERT: H 400 TYR cc_start: 0.7868 (m-80) cc_final: 0.7460 (m-80) REVERT: H 401 PHE cc_start: 0.8246 (p90) cc_final: 0.8017 (p90) REVERT: H 441 GLN cc_start: 0.8560 (mm-40) cc_final: 0.8318 (mm-40) REVERT: H 482 MET cc_start: 0.8446 (tpt) cc_final: 0.8088 (tpt) REVERT: H 484 TYR cc_start: 0.8992 (m-10) cc_final: 0.8155 (m-10) REVERT: H 487 GLU cc_start: 0.8560 (pm20) cc_final: 0.8161 (pm20) REVERT: H 490 PHE cc_start: 0.8239 (m-80) cc_final: 0.7870 (m-80) REVERT: H 514 PHE cc_start: 0.7189 (p90) cc_final: 0.6923 (p90) outliers start: 246 outliers final: 114 residues processed: 1175 average time/residue: 0.1801 time to fit residues: 344.6293 Evaluate side-chains 1070 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 919 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 382 SER Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 466 HIS Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 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 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 382 SER Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 466 HIS Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 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: 3.9990 chunk 67 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 275 optimal weight: 4.9990 chunk 225 optimal weight: 0.0270 chunk 171 optimal weight: 3.9990 chunk 299 optimal weight: 20.0000 chunk 325 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 overall best weight: 3.2046 ------------------------------------------------------------------------------- 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 303 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 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 E 465 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 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 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 303 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4159 r_free = 0.4159 target = 0.164453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.124259 restraints weight = 51815.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.129816 restraints weight = 30191.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.133736 restraints weight = 20853.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.136495 restraints weight = 15871.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.138627 restraints weight = 12908.077| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3154 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= 0.242 Angle : 0.865 13.811 42888 Z= 0.422 Chirality : 0.051 0.149 4888 Planarity : 0.005 0.049 5328 Dihedral : 18.135 179.048 4723 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 9.21 % Allowed : 24.40 % Favored : 66.38 % 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: -2.57 (0.13), residues: 3880 helix: -1.86 (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 0.008 0.001 ARG B 149 TYR 0.029 0.002 TYR H 233 PHE 0.018 0.002 PHE D 90 HIS 0.006 0.001 HIS H 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.24 (31576) covalent geometry : angle 0.86502 / 0.42 (42888) hydrogen bonds : bond 0.04313 / 2.86 ( 832) hydrogen bonds : angle 5.79050 / 4.00 ( 2376) Misc. bond : bond 0.00036 / 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 1330 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 294 poor density : 1036 time to evaluate : 0.979 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: 0.8648 (m-80) cc_final: 0.8374 (m-10) REVERT: A 165 PHE cc_start: 0.8172 (p90) cc_final: 0.7953 (p90) REVERT: A 202 GLN cc_start: 0.9358 (mt0) cc_final: 0.8873 (mt0) REVERT: A 206 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8038 (ttpt) REVERT: A 250 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7929 (pp) REVERT: A 254 GLU cc_start: 0.9407 (pp20) cc_final: 0.9116 (pm20) REVERT: A 258 TYR cc_start: 0.8751 (t80) cc_final: 0.8532 (t80) REVERT: A 285 ASN cc_start: 0.9479 (m110) cc_final: 0.9179 (m110) REVERT: A 297 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8859 (tm) REVERT: A 311 LYS cc_start: 0.8800 (tmtt) cc_final: 0.7925 (tppt) REVERT: A 337 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7285 (tt) REVERT: A 386 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8121 (ppp) REVERT: A 470 ASP cc_start: 0.8608 (m-30) cc_final: 0.8297 (m-30) REVERT: A 482 MET cc_start: 0.8708 (tpt) cc_final: 0.8462 (tpt) REVERT: A 487 GLU cc_start: 0.8436 (pm20) cc_final: 0.7973 (pm20) REVERT: A 488 LEU cc_start: 0.8515 (tm) cc_final: 0.8236 (tm) REVERT: A 490 PHE cc_start: 0.8428 (m-80) cc_final: 0.8083 (m-80) REVERT: B 65 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9030 (pt) REVERT: B 165 PHE cc_start: 0.8029 (p90) cc_final: 0.7786 (p90) REVERT: B 176 GLU cc_start: 0.9179 (mp0) cc_final: 0.8875 (mp0) REVERT: B 199 GLU cc_start: 0.9320 (tp30) cc_final: 0.8981 (tp30) REVERT: B 202 GLN cc_start: 0.9303 (mt0) cc_final: 0.8956 (mt0) REVERT: B 206 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8143 (ttpt) REVERT: B 216 ASP cc_start: 0.9045 (t70) cc_final: 0.8670 (t0) REVERT: B 250 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7830 (pp) REVERT: B 265 GLN cc_start: 0.9305 (mm110) cc_final: 0.9064 (mm-40) REVERT: B 311 LYS cc_start: 0.8941 (tmtt) cc_final: 0.8433 (tptt) REVERT: B 337 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7282 (tt) REVERT: B 385 MET cc_start: 0.8626 (ttp) cc_final: 0.8396 (ttp) REVERT: B 386 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8323 (pmm) REVERT: B 407 ARG cc_start: 0.7381 (ttt180) cc_final: 0.7074 (ttt90) REVERT: B 412 ARG cc_start: 0.7361 (pmt-80) cc_final: 0.7076 (pmt-80) REVERT: B 420 MET cc_start: 0.6851 (mmm) cc_final: 0.6471 (mmm) REVERT: B 470 ASP cc_start: 0.8599 (m-30) cc_final: 0.8186 (m-30) REVERT: B 482 MET cc_start: 0.8639 (tpt) cc_final: 0.8301 (tpt) REVERT: B 487 GLU cc_start: 0.8601 (pm20) cc_final: 0.8262 (pm20) REVERT: B 490 PHE cc_start: 0.8396 (m-80) cc_final: 0.7897 (m-80) REVERT: C 32 TYR cc_start: 0.8678 (m-80) cc_final: 0.8396 (m-10) REVERT: C 73 VAL cc_start: 0.8500 (OUTLIER) cc_final: 0.6912 (t) REVERT: C 78 MET cc_start: 0.8245 (ttm) cc_final: 0.8002 (ttt) REVERT: C 128 ARG cc_start: 0.8798 (mmt90) cc_final: 0.8541 (mmt90) REVERT: C 165 PHE cc_start: 0.8059 (p90) cc_final: 0.7855 (p90) REVERT: C 199 GLU cc_start: 0.9508 (tp30) cc_final: 0.9202 (tp30) REVERT: C 206 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8027 (ttpt) REVERT: C 208 LYS cc_start: 0.8663 (mtpp) cc_final: 0.8427 (ttmm) REVERT: C 216 ASP cc_start: 0.9095 (t70) cc_final: 0.8733 (t0) REVERT: C 235 LEU cc_start: 0.9158 (mt) cc_final: 0.8950 (mt) REVERT: C 250 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7805 (pp) REVERT: C 261 ASP cc_start: 0.8793 (m-30) cc_final: 0.8451 (p0) REVERT: C 265 GLN cc_start: 0.9319 (mm110) cc_final: 0.9082 (mm-40) REVERT: C 297 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8754 (tm) REVERT: C 311 LYS cc_start: 0.8803 (tmtt) cc_final: 0.7939 (tppt) REVERT: C 337 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7155 (tt) REVERT: C 386 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8085 (ppp) REVERT: C 412 ARG cc_start: 0.7455 (pmt-80) cc_final: 0.7239 (pmt-80) REVERT: C 420 MET cc_start: 0.6567 (mmm) cc_final: 0.6129 (mmm) REVERT: C 470 ASP cc_start: 0.8624 (m-30) cc_final: 0.8292 (m-30) REVERT: C 482 MET cc_start: 0.8730 (tpt) cc_final: 0.8479 (tpt) REVERT: C 487 GLU cc_start: 0.8580 (pm20) cc_final: 0.8148 (pm20) REVERT: C 490 PHE cc_start: 0.8487 (m-80) cc_final: 0.8137 (m-80) REVERT: C 509 TYR cc_start: 0.7689 (p90) cc_final: 0.7417 (p90) REVERT: C 510 GLU cc_start: 0.6747 (mm-30) cc_final: 0.6394 (mm-30) REVERT: C 514 PHE cc_start: 0.7553 (p90) cc_final: 0.7222 (p90) REVERT: D 32 TYR cc_start: 0.8579 (m-10) cc_final: 0.8336 (m-10) REVERT: D 73 VAL cc_start: 0.8282 (OUTLIER) cc_final: 0.6726 (t) REVERT: D 78 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7904 (ttt) REVERT: D 128 ARG cc_start: 0.8838 (mmt90) cc_final: 0.8578 (ttm-80) REVERT: D 165 PHE cc_start: 0.8047 (p90) cc_final: 0.7792 (p90) REVERT: D 176 GLU cc_start: 0.9241 (mp0) cc_final: 0.8966 (mp0) REVERT: D 199 GLU cc_start: 0.9510 (tp30) cc_final: 0.9227 (tp30) REVERT: D 206 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8043 (ttpt) REVERT: D 216 ASP cc_start: 0.9074 (t70) cc_final: 0.8715 (t0) REVERT: D 265 GLN cc_start: 0.9327 (mm110) cc_final: 0.9108 (mm-40) REVERT: D 297 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8889 (tm) REVERT: D 311 LYS cc_start: 0.8907 (tmtt) cc_final: 0.8379 (tptt) REVERT: D 337 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7296 (tt) REVERT: D 386 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8496 (pmm) REVERT: D 390 LEU cc_start: 0.9117 (tt) cc_final: 0.8603 (tt) REVERT: D 400 TYR cc_start: 0.7817 (m-80) cc_final: 0.7523 (m-80) REVERT: D 420 MET cc_start: 0.6740 (mmm) cc_final: 0.6347 (mmm) REVERT: D 470 ASP cc_start: 0.8706 (m-30) cc_final: 0.8324 (m-30) REVERT: D 482 MET cc_start: 0.8672 (tpt) cc_final: 0.8410 (tpt) REVERT: D 487 GLU cc_start: 0.8572 (pm20) cc_final: 0.8130 (pm20) REVERT: D 490 PHE cc_start: 0.8377 (m-80) cc_final: 0.8021 (m-80) REVERT: D 510 GLU cc_start: 0.6762 (mm-30) cc_final: 0.6509 (mm-30) REVERT: D 514 PHE cc_start: 0.7587 (p90) cc_final: 0.7236 (p90) REVERT: E 78 MET cc_start: 0.8506 (ttm) cc_final: 0.8099 (ttt) REVERT: E 165 PHE cc_start: 0.8192 (p90) cc_final: 0.7665 (p90) REVERT: E 185 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7550 (mt) REVERT: E 206 LYS cc_start: 0.8215 (tppt) cc_final: 0.7773 (tppt) REVERT: E 216 ASP cc_start: 0.9101 (t70) cc_final: 0.8742 (t0) REVERT: E 235 LEU cc_start: 0.9179 (mt) cc_final: 0.8954 (mt) REVERT: E 250 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7848 (pp) REVERT: E 297 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8859 (tm) REVERT: E 311 LYS cc_start: 0.8892 (tmtt) cc_final: 0.8435 (tptt) REVERT: E 337 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7141 (tt) REVERT: E 385 MET cc_start: 0.8383 (ttp) cc_final: 0.7986 (ttp) REVERT: E 386 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8125 (ppp) REVERT: E 420 MET cc_start: 0.6728 (mmm) cc_final: 0.6333 (mmm) REVERT: E 470 ASP cc_start: 0.8620 (m-30) cc_final: 0.8208 (m-30) REVERT: E 482 MET cc_start: 0.8647 (tpt) cc_final: 0.8414 (tpt) REVERT: E 487 GLU cc_start: 0.8645 (pm20) cc_final: 0.8203 (pm20) REVERT: E 490 PHE cc_start: 0.8416 (m-80) cc_final: 0.7996 (m-80) REVERT: E 509 TYR cc_start: 0.7860 (p90) cc_final: 0.7579 (p90) REVERT: E 510 GLU cc_start: 0.6740 (mm-30) cc_final: 0.6414 (mm-30) REVERT: F 62 LYS cc_start: 0.9304 (mmtp) cc_final: 0.8850 (mttm) REVERT: F 78 MET cc_start: 0.8584 (ttm) cc_final: 0.8181 (ttt) REVERT: F 165 PHE cc_start: 0.8258 (p90) cc_final: 0.7648 (p90) REVERT: F 176 GLU cc_start: 0.9210 (mp0) cc_final: 0.8930 (mp0) REVERT: F 199 GLU cc_start: 0.9537 (tp30) cc_final: 0.9192 (tp30) REVERT: F 206 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8084 (ttpt) REVERT: F 216 ASP cc_start: 0.9085 (t70) cc_final: 0.8746 (t0) REVERT: F 235 LEU cc_start: 0.9164 (mt) cc_final: 0.8543 (mt) REVERT: F 243 GLN cc_start: 0.8694 (mp-120) cc_final: 0.8217 (mp10) REVERT: F 265 GLN cc_start: 0.9326 (mm110) cc_final: 0.9067 (mm-40) REVERT: F 297 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8891 (tm) REVERT: F 311 LYS cc_start: 0.8878 (tmtt) cc_final: 0.8395 (tptt) REVERT: F 337 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7170 (tt) REVERT: F 379 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9178 (tm) REVERT: F 386 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8216 (ppp) REVERT: F 390 LEU cc_start: 0.9165 (tt) cc_final: 0.8961 (tt) REVERT: F 470 ASP cc_start: 0.8706 (m-30) cc_final: 0.8260 (m-30) REVERT: F 482 MET cc_start: 0.8698 (tpt) cc_final: 0.8372 (tpt) REVERT: F 487 GLU cc_start: 0.8690 (pm20) cc_final: 0.8350 (pm20) REVERT: F 490 PHE cc_start: 0.8478 (m-80) cc_final: 0.7953 (m-80) REVERT: F 509 TYR cc_start: 0.7856 (p90) cc_final: 0.7584 (p90) REVERT: F 510 GLU cc_start: 0.6641 (mm-30) cc_final: 0.6171 (mm-30) REVERT: F 514 PHE cc_start: 0.7623 (p90) cc_final: 0.7287 (p90) REVERT: G 32 TYR cc_start: 0.8634 (m-80) cc_final: 0.8404 (m-10) REVERT: G 165 PHE cc_start: 0.8118 (p90) cc_final: 0.7858 (p90) REVERT: G 199 GLU cc_start: 0.9507 (tp30) cc_final: 0.9105 (tp30) REVERT: G 203 ARG cc_start: 0.9360 (ptp-110) cc_final: 0.9070 (ptp-110) REVERT: G 206 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8076 (ttpt) REVERT: G 250 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.7950 (pp) REVERT: G 258 TYR cc_start: 0.8644 (t80) cc_final: 0.8408 (t80) REVERT: G 297 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8853 (tm) REVERT: G 311 LYS cc_start: 0.8889 (tmtt) cc_final: 0.8072 (tppt) REVERT: G 337 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7221 (tt) REVERT: G 385 MET cc_start: 0.8429 (ttp) cc_final: 0.7987 (ttp) REVERT: G 386 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8148 (ppp) REVERT: G 400 TYR cc_start: 0.7613 (m-80) cc_final: 0.7383 (m-80) REVERT: G 407 ARG cc_start: 0.7357 (ttt180) cc_final: 0.6500 (ttt90) REVERT: G 420 MET cc_start: 0.6729 (mmm) cc_final: 0.6352 (mmm) REVERT: G 470 ASP cc_start: 0.8619 (m-30) cc_final: 0.8364 (m-30) REVERT: G 482 MET cc_start: 0.8688 (tpt) cc_final: 0.8342 (tpt) REVERT: G 487 GLU cc_start: 0.8688 (pm20) cc_final: 0.8357 (pm20) REVERT: G 490 PHE cc_start: 0.8414 (m-80) cc_final: 0.8019 (m-80) REVERT: G 509 TYR cc_start: 0.7877 (p90) cc_final: 0.7501 (p90) REVERT: G 510 GLU cc_start: 0.6834 (mm-30) cc_final: 0.6353 (mm-30) REVERT: H 32 TYR cc_start: 0.8454 (m-10) cc_final: 0.8177 (m-10) REVERT: H 62 LYS cc_start: 0.9342 (mmtp) cc_final: 0.8871 (mttm) REVERT: H 65 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9079 (pt) REVERT: H 66 VAL cc_start: 0.8913 (OUTLIER) cc_final: 0.8566 (p) REVERT: H 73 VAL cc_start: 0.8465 (OUTLIER) cc_final: 0.7109 (t) REVERT: H 136 ARG cc_start: 0.9021 (ptp-110) cc_final: 0.8728 (ptp90) REVERT: H 165 PHE cc_start: 0.8142 (p90) cc_final: 0.7843 (p90) REVERT: H 199 GLU cc_start: 0.9506 (tp30) cc_final: 0.9245 (tp30) REVERT: H 206 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8003 (ttpt) REVERT: H 216 ASP cc_start: 0.8967 (t70) cc_final: 0.8604 (t0) REVERT: H 235 LEU cc_start: 0.9169 (mt) cc_final: 0.8529 (mt) REVERT: H 250 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8013 (pp) REVERT: H 297 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8898 (tm) REVERT: H 311 LYS cc_start: 0.8876 (tmtt) cc_final: 0.8382 (tptt) REVERT: H 337 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7342 (tt) REVERT: H 379 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9115 (tm) REVERT: H 386 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8182 (pmm) REVERT: H 401 PHE cc_start: 0.8252 (p90) cc_final: 0.7942 (p90) REVERT: H 441 GLN cc_start: 0.8512 (mm-40) cc_final: 0.8305 (mm-40) REVERT: H 470 ASP cc_start: 0.8755 (m-30) cc_final: 0.8330 (m-30) REVERT: H 482 MET cc_start: 0.8634 (tpt) cc_final: 0.8365 (tpt) REVERT: H 487 GLU cc_start: 0.8573 (pm20) cc_final: 0.8126 (pm20) REVERT: H 490 PHE cc_start: 0.8390 (m-80) cc_final: 0.7899 (m-80) REVERT: H 509 TYR cc_start: 0.7978 (p90) cc_final: 0.7737 (p90) REVERT: H 514 PHE cc_start: 0.7651 (p90) cc_final: 0.7288 (p90) outliers start: 294 outliers final: 178 residues processed: 1170 average time/residue: 0.1865 time to fit residues: 352.1834 Evaluate side-chains 1160 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 936 time to evaluate : 1.226 ------------------------------------------------------------------------------- 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 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 382 SER Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain 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 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 345 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 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 362 ILE 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 72 THR 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 186 VAL Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 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 238 LYS Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 294 TYR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain 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 235 LEU 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 286 MET Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 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 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 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 345 THR 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: 2.9990 chunk 100 optimal weight: 7.9990 chunk 237 optimal weight: 0.6980 chunk 185 optimal weight: 7.9990 chunk 323 optimal weight: 0.9990 chunk 304 optimal weight: 4.9990 chunk 282 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 303 ASN B 309 GLN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** 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 ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN F 171 HIS ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 GLN F 303 ASN F 309 GLN ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 465 GLN G 171 HIS ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 309 GLN ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 GLN G 498 GLN H 171 HIS ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 GLN ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.168249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.128859 restraints weight = 50620.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.134665 restraints weight = 29077.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.138729 restraints weight = 19806.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.141660 restraints weight = 14913.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.143745 restraints weight = 11989.533| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 31592 Z= 0.158 Angle : 0.823 13.778 42888 Z= 0.389 Chirality : 0.049 0.181 4888 Planarity : 0.004 0.050 5328 Dihedral : 16.339 152.069 4711 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 9.30 % Allowed : 26.07 % Favored : 64.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.13), residues: 3880 helix: -1.63 (0.13), residues: 1296 sheet: -2.30 (0.20), residues: 520 loop : -1.25 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 182 TYR 0.030 0.002 TYR G 484 PHE 0.014 0.001 PHE H 456 HIS 0.004 0.001 HIS D 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (31576) covalent geometry : angle 0.82315 / 0.39 (42888) hydrogen bonds : bond 0.03717 / 2.43 ( 832) hydrogen bonds : angle 5.50636 / 3.81 ( 2376) Misc. bond : bond 0.00037 / 0.03 ( 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 1347 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 297 poor density : 1050 time to evaluate : 1.307 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: 0.8591 (m-80) cc_final: 0.8367 (m-10) REVERT: A 51 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8003 (pp) REVERT: A 128 ARG cc_start: 0.8860 (mmt90) cc_final: 0.8574 (mmt90) REVERT: A 165 PHE cc_start: 0.8119 (p90) cc_final: 0.7879 (p90) REVERT: A 206 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7986 (ttpt) REVERT: A 208 LYS cc_start: 0.8210 (ttmm) cc_final: 0.7945 (mtpp) REVERT: A 230 ASN cc_start: 0.8623 (t0) cc_final: 0.8319 (t0) REVERT: A 250 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7818 (pp) REVERT: A 254 GLU cc_start: 0.9376 (pp20) cc_final: 0.9136 (pm20) REVERT: A 285 ASN cc_start: 0.9478 (m110) cc_final: 0.9195 (m110) REVERT: A 297 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8820 (tm) REVERT: A 311 LYS cc_start: 0.8738 (tmtt) cc_final: 0.7889 (tppt) REVERT: A 337 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7199 (tt) REVERT: A 386 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8299 (pmm) REVERT: A 420 MET cc_start: 0.6704 (mmm) cc_final: 0.6318 (mmm) REVERT: A 455 LYS cc_start: 0.8630 (mttp) cc_final: 0.8420 (mtmm) REVERT: A 470 ASP cc_start: 0.8678 (m-30) cc_final: 0.8286 (m-30) REVERT: A 482 MET cc_start: 0.8726 (tpt) cc_final: 0.8461 (tpt) REVERT: A 487 GLU cc_start: 0.8375 (pm20) cc_final: 0.7931 (pm20) REVERT: A 488 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8148 (tm) REVERT: A 490 PHE cc_start: 0.8456 (m-80) cc_final: 0.8086 (m-80) REVERT: A 509 TYR cc_start: 0.7755 (p90) cc_final: 0.7451 (p90) REVERT: B 109 LYS cc_start: 0.8704 (mmtm) cc_final: 0.8378 (mptt) REVERT: B 128 ARG cc_start: 0.9137 (mmm-85) cc_final: 0.8802 (mmt90) REVERT: B 165 PHE cc_start: 0.7952 (p90) cc_final: 0.7704 (p90) REVERT: B 206 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8145 (ttpt) REVERT: B 216 ASP cc_start: 0.9015 (t70) cc_final: 0.8635 (t0) REVERT: B 261 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8416 (p0) REVERT: B 283 GLN cc_start: 0.8780 (tt0) cc_final: 0.8526 (mt0) REVERT: B 311 LYS cc_start: 0.8864 (tmtt) cc_final: 0.8337 (tptt) REVERT: B 337 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7224 (tt) REVERT: B 385 MET cc_start: 0.8477 (ttp) cc_final: 0.8181 (ttp) REVERT: B 386 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8294 (pmm) REVERT: B 407 ARG cc_start: 0.7515 (ttt180) cc_final: 0.7230 (ttt180) REVERT: B 420 MET cc_start: 0.6858 (mmm) cc_final: 0.6451 (mmm) REVERT: B 470 ASP cc_start: 0.8744 (m-30) cc_final: 0.8324 (m-30) REVERT: B 482 MET cc_start: 0.8726 (tpt) cc_final: 0.8385 (tpt) REVERT: B 487 GLU cc_start: 0.8572 (pm20) cc_final: 0.8305 (pm20) REVERT: B 490 PHE cc_start: 0.8373 (m-80) cc_final: 0.7875 (m-80) REVERT: B 509 TYR cc_start: 0.7408 (p90) cc_final: 0.7011 (p90) REVERT: C 32 TYR cc_start: 0.8620 (m-80) cc_final: 0.8394 (m-10) REVERT: C 109 LYS cc_start: 0.8737 (mmtm) cc_final: 0.8422 (mptt) REVERT: C 165 PHE cc_start: 0.8086 (p90) cc_final: 0.7853 (p90) REVERT: C 199 GLU cc_start: 0.9503 (tp30) cc_final: 0.9245 (tp30) REVERT: C 203 ARG cc_start: 0.9371 (ptp-110) cc_final: 0.9150 (ptp-110) REVERT: C 206 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8045 (ttpt) REVERT: C 208 LYS cc_start: 0.8699 (mtpp) cc_final: 0.8007 (mtpp) REVERT: C 235 LEU cc_start: 0.9084 (mt) cc_final: 0.8865 (mt) REVERT: C 250 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7680 (pp) REVERT: C 258 TYR cc_start: 0.8544 (t80) cc_final: 0.8152 (t80) REVERT: C 297 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8825 (tm) REVERT: C 311 LYS cc_start: 0.8718 (tmtt) cc_final: 0.7881 (tppt) REVERT: C 337 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7242 (tt) REVERT: C 386 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8366 (ppp) REVERT: C 400 TYR cc_start: 0.7524 (m-80) cc_final: 0.7201 (m-80) REVERT: C 407 ARG cc_start: 0.7252 (ttt180) cc_final: 0.6991 (ttt90) REVERT: C 420 MET cc_start: 0.6650 (mmm) cc_final: 0.6210 (mmm) REVERT: C 470 ASP cc_start: 0.8666 (m-30) cc_final: 0.8262 (m-30) REVERT: C 482 MET cc_start: 0.8714 (tpt) cc_final: 0.8473 (tpt) REVERT: C 487 GLU cc_start: 0.8488 (pm20) cc_final: 0.8038 (pm20) REVERT: C 488 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8032 (tm) REVERT: C 490 PHE cc_start: 0.8412 (m-80) cc_final: 0.8106 (m-80) REVERT: C 509 TYR cc_start: 0.7721 (p90) cc_final: 0.7433 (p90) REVERT: C 510 GLU cc_start: 0.6998 (mm-30) cc_final: 0.6667 (mm-30) REVERT: D 73 VAL cc_start: 0.8185 (OUTLIER) cc_final: 0.6722 (t) REVERT: D 78 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7905 (ttt) REVERT: D 165 PHE cc_start: 0.7946 (p90) cc_final: 0.7702 (p90) REVERT: D 199 GLU cc_start: 0.9472 (tp30) cc_final: 0.9261 (tp30) REVERT: D 206 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8075 (ttpt) REVERT: D 216 ASP cc_start: 0.9065 (t70) cc_final: 0.8698 (t0) REVERT: D 297 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8905 (tm) REVERT: D 309 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8855 (pt0) REVERT: D 311 LYS cc_start: 0.8823 (tmtt) cc_final: 0.7899 (tppt) REVERT: D 337 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7296 (tt) REVERT: D 386 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8163 (pmm) REVERT: D 390 LEU cc_start: 0.9059 (tt) cc_final: 0.8496 (tt) REVERT: D 400 TYR cc_start: 0.7819 (m-80) cc_final: 0.7477 (m-80) REVERT: D 407 ARG cc_start: 0.7250 (ttt180) cc_final: 0.6624 (ttt180) REVERT: D 420 MET cc_start: 0.6746 (mmm) cc_final: 0.6333 (mmm) REVERT: D 470 ASP cc_start: 0.8774 (m-30) cc_final: 0.8377 (m-30) REVERT: D 482 MET cc_start: 0.8692 (tpt) cc_final: 0.8412 (tpt) REVERT: D 487 GLU cc_start: 0.8553 (pm20) cc_final: 0.8188 (pm20) REVERT: D 490 PHE cc_start: 0.8349 (m-80) cc_final: 0.7896 (m-80) REVERT: D 509 TYR cc_start: 0.7425 (p90) cc_final: 0.7016 (p90) REVERT: D 510 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6773 (mm-30) REVERT: E 65 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8949 (pt) REVERT: E 78 MET cc_start: 0.8271 (ttm) cc_final: 0.7897 (ttt) REVERT: E 109 LYS cc_start: 0.8796 (mmtm) cc_final: 0.8462 (mptt) REVERT: E 128 ARG cc_start: 0.9137 (mmm-85) cc_final: 0.8745 (mmt90) REVERT: E 165 PHE cc_start: 0.8123 (p90) cc_final: 0.7864 (p90) REVERT: E 185 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7489 (mt) REVERT: E 203 ARG cc_start: 0.9285 (ptp-110) cc_final: 0.9081 (ptp-110) REVERT: E 206 LYS cc_start: 0.8265 (tppt) cc_final: 0.7887 (tppt) REVERT: E 216 ASP cc_start: 0.9133 (t70) cc_final: 0.8769 (t0) REVERT: E 235 LEU cc_start: 0.9132 (mt) cc_final: 0.8892 (mt) REVERT: E 250 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7672 (pp) REVERT: E 258 TYR cc_start: 0.8533 (t80) cc_final: 0.8325 (t80) REVERT: E 297 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8756 (tm) REVERT: E 311 LYS cc_start: 0.8838 (tmtt) cc_final: 0.8366 (tptt) REVERT: E 337 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7162 (tt) REVERT: E 355 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8421 (ttm110) REVERT: E 385 MET cc_start: 0.8410 (ttp) cc_final: 0.8109 (ttp) REVERT: E 386 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8337 (ppp) REVERT: E 400 TYR cc_start: 0.7606 (m-80) cc_final: 0.7315 (m-80) REVERT: E 407 ARG cc_start: 0.7324 (ttt180) cc_final: 0.5916 (ttt180) REVERT: E 420 MET cc_start: 0.6722 (mmm) cc_final: 0.6338 (mmm) REVERT: E 470 ASP cc_start: 0.8720 (m-30) cc_final: 0.8330 (m-30) REVERT: E 482 MET cc_start: 0.8650 (tpt) cc_final: 0.8417 (tpt) REVERT: E 484 TYR cc_start: 0.8945 (m-10) cc_final: 0.8663 (m-10) REVERT: E 487 GLU cc_start: 0.8574 (pm20) cc_final: 0.8186 (pm20) REVERT: E 488 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7963 (tm) REVERT: E 489 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8001 (tttt) REVERT: E 490 PHE cc_start: 0.8466 (m-80) cc_final: 0.8112 (m-80) REVERT: E 509 TYR cc_start: 0.7838 (p90) cc_final: 0.7493 (p90) REVERT: E 510 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6630 (mm-30) REVERT: F 62 LYS cc_start: 0.9266 (mmtp) cc_final: 0.8784 (mttm) REVERT: F 78 MET cc_start: 0.8457 (ttm) cc_final: 0.8071 (ttt) REVERT: F 132 GLU cc_start: 0.9483 (mp0) cc_final: 0.9257 (mp0) REVERT: F 165 PHE cc_start: 0.8263 (p90) cc_final: 0.7967 (p90) REVERT: F 166 LEU cc_start: 0.8218 (tp) cc_final: 0.7933 (tp) REVERT: F 199 GLU cc_start: 0.9511 (tp30) cc_final: 0.9293 (tp30) REVERT: F 206 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8122 (ttpt) REVERT: F 216 ASP cc_start: 0.9086 (t70) cc_final: 0.8720 (t0) REVERT: F 235 LEU cc_start: 0.9084 (mt) cc_final: 0.8452 (mt) REVERT: F 261 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8330 (p0) REVERT: F 297 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8840 (tm) REVERT: F 309 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8879 (pt0) REVERT: F 311 LYS cc_start: 0.8803 (tmtt) cc_final: 0.8309 (tptt) REVERT: F 337 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7295 (tt) REVERT: F 352 GLU cc_start: 0.8887 (tp30) cc_final: 0.8491 (tp30) REVERT: F 385 MET cc_start: 0.8522 (ttp) cc_final: 0.8295 (ttp) REVERT: F 386 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8159 (pmm) REVERT: F 390 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8600 (tt) REVERT: F 399 GLU cc_start: 0.8853 (pm20) cc_final: 0.8134 (tt0) REVERT: F 407 ARG cc_start: 0.7585 (ttt180) cc_final: 0.7242 (ttt90) REVERT: F 408 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8724 (mp) REVERT: F 470 ASP cc_start: 0.8812 (m-30) cc_final: 0.8441 (m-30) REVERT: F 482 MET cc_start: 0.8804 (tpt) cc_final: 0.8479 (tpt) REVERT: F 484 TYR cc_start: 0.9026 (m-10) cc_final: 0.8736 (m-80) REVERT: F 487 GLU cc_start: 0.8664 (pm20) cc_final: 0.8369 (pm20) REVERT: F 488 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7999 (tm) REVERT: F 489 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7932 (tttt) REVERT: F 490 PHE cc_start: 0.8398 (m-80) cc_final: 0.7981 (m-80) REVERT: F 509 TYR cc_start: 0.7839 (p90) cc_final: 0.7542 (p90) REVERT: F 510 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6363 (mm-30) REVERT: F 514 PHE cc_start: 0.7511 (p90) cc_final: 0.7112 (p90) REVERT: G 32 TYR cc_start: 0.8608 (m-80) cc_final: 0.8358 (m-10) REVERT: G 65 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8993 (pt) REVERT: G 78 MET cc_start: 0.7561 (ttp) cc_final: 0.7170 (ttp) REVERT: G 109 LYS cc_start: 0.8801 (mmtm) cc_final: 0.8424 (mptt) REVERT: G 165 PHE cc_start: 0.8078 (p90) cc_final: 0.7769 (p90) REVERT: G 199 GLU cc_start: 0.9496 (tp30) cc_final: 0.9231 (tp30) REVERT: G 206 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7985 (ttpt) REVERT: G 208 LYS cc_start: 0.8083 (ttmm) cc_final: 0.7693 (ttmm) REVERT: G 297 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8850 (tm) REVERT: G 311 LYS cc_start: 0.8786 (tmtt) cc_final: 0.8017 (tppt) REVERT: G 337 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7238 (tt) REVERT: G 386 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8417 (pmm) REVERT: G 400 TYR cc_start: 0.7582 (m-80) cc_final: 0.7218 (m-80) REVERT: G 407 ARG cc_start: 0.7364 (ttt180) cc_final: 0.6800 (ttt90) REVERT: G 470 ASP cc_start: 0.8734 (m-30) cc_final: 0.8345 (m-30) REVERT: G 482 MET cc_start: 0.8774 (tpt) cc_final: 0.8519 (tpt) REVERT: G 487 GLU cc_start: 0.8651 (pm20) cc_final: 0.8267 (pm20) REVERT: G 488 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8025 (tm) REVERT: G 489 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7954 (tttt) REVERT: G 490 PHE cc_start: 0.8497 (m-80) cc_final: 0.8077 (m-80) REVERT: G 509 TYR cc_start: 0.7936 (p90) cc_final: 0.7625 (p90) REVERT: G 510 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6770 (mm-30) REVERT: H 62 LYS cc_start: 0.9272 (mmtp) cc_final: 0.8768 (mttm) REVERT: H 78 MET cc_start: 0.7803 (ttt) cc_final: 0.7415 (ttt) REVERT: H 109 LYS cc_start: 0.8755 (mmtm) cc_final: 0.8406 (mptt) REVERT: H 161 ARG cc_start: 0.9615 (mpp-170) cc_final: 0.8774 (mtt90) REVERT: H 165 PHE cc_start: 0.8056 (p90) cc_final: 0.7806 (p90) REVERT: H 199 GLU cc_start: 0.9500 (tp30) cc_final: 0.9253 (tp30) REVERT: H 206 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8027 (ttpt) REVERT: H 216 ASP cc_start: 0.8980 (t70) cc_final: 0.8611 (t0) REVERT: H 235 LEU cc_start: 0.9107 (mt) cc_final: 0.8437 (mt) REVERT: H 261 ASP cc_start: 0.8631 (m-30) cc_final: 0.8413 (m-30) REVERT: H 283 GLN cc_start: 0.8787 (tt0) cc_final: 0.8523 (mt0) REVERT: H 297 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8831 (tm) REVERT: H 309 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8751 (pt0) REVERT: H 311 LYS cc_start: 0.8781 (tmtt) cc_final: 0.8282 (tptt) REVERT: H 337 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7243 (tt) REVERT: H 348 TYR cc_start: 0.9139 (t80) cc_final: 0.8857 (t80) REVERT: H 352 GLU cc_start: 0.8814 (tp30) cc_final: 0.8524 (tp30) REVERT: H 386 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8085 (pmm) REVERT: H 401 PHE cc_start: 0.8224 (p90) cc_final: 0.7943 (p90) REVERT: H 470 ASP cc_start: 0.8818 (m-30) cc_final: 0.8461 (m-30) REVERT: H 482 MET cc_start: 0.8692 (tpt) cc_final: 0.8431 (tpt) REVERT: H 487 GLU cc_start: 0.8565 (pm20) cc_final: 0.8155 (pm20) REVERT: H 489 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7847 (tttt) REVERT: H 490 PHE cc_start: 0.8311 (m-80) cc_final: 0.7889 (m-80) REVERT: H 509 TYR cc_start: 0.8004 (p90) cc_final: 0.7795 (p90) outliers start: 297 outliers final: 174 residues processed: 1188 average time/residue: 0.1915 time to fit residues: 364.9071 Evaluate side-chains 1181 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 231 poor density : 950 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 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 386 MET Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain 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 327 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain C residue 19 THR 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 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 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 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 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 61 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 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 336 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 362 ILE 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 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 314 ILE Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 355 ARG Chi-restraints excluded: chain E residue 361 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 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 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 386 MET Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 489 LYS 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 238 LYS Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain G residue 498 GLN Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 222 ILE Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 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 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 489 LYS Chi-restraints excluded: chain H residue 494 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 104 optimal weight: 0.5980 chunk 162 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 225 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 343 optimal weight: 7.9990 chunk 290 optimal weight: 1.9990 chunk 197 optimal weight: 0.0870 chunk 18 optimal weight: 0.1980 chunk 282 optimal weight: 9.9990 overall best weight: 0.4960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 HIS ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN E 303 ASN ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 GLN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 465 GLN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.168406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.131220 restraints weight = 51004.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.136906 restraints weight = 29181.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.140867 restraints weight = 19773.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.143743 restraints weight = 14784.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.145714 restraints weight = 11799.908| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31592 Z= 0.132 Angle : 0.846 12.781 42888 Z= 0.390 Chirality : 0.049 0.177 4888 Planarity : 0.005 0.051 5328 Dihedral : 14.489 146.403 4695 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 8.21 % Allowed : 27.98 % Favored : 63.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.13), residues: 3880 helix: -1.41 (0.14), residues: 1240 sheet: -2.32 (0.20), residues: 520 loop : -1.20 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 231 TYR 0.027 0.002 TYR G 484 PHE 0.020 0.001 PHE E 90 HIS 0.003 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (31576) covalent geometry : angle 0.84552 / 0.39 (42888) hydrogen bonds : bond 0.03532 / 2.29 ( 832) hydrogen bonds : angle 5.38531 / 3.73 ( 2376) Misc. bond : bond 0.00035 / 0.02 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1358 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 262 poor density : 1096 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7997 (pp) REVERT: A 109 LYS cc_start: 0.8848 (mmtm) cc_final: 0.8629 (mmtm) REVERT: A 128 ARG cc_start: 0.8845 (mmt90) cc_final: 0.8552 (mmt90) REVERT: A 250 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7537 (pp) REVERT: A 297 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8702 (tm) REVERT: A 311 LYS cc_start: 0.8752 (tmtt) cc_final: 0.7871 (tppt) REVERT: A 337 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7123 (tt) REVERT: A 355 ARG cc_start: 0.8371 (ttm170) cc_final: 0.7991 (mtp180) REVERT: A 386 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8337 (pmm) REVERT: A 420 MET cc_start: 0.6647 (mmm) cc_final: 0.6344 (mmm) REVERT: A 469 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.7658 (pt0) REVERT: A 470 ASP cc_start: 0.8633 (m-30) cc_final: 0.8353 (m-30) REVERT: A 482 MET cc_start: 0.8601 (tpt) cc_final: 0.8341 (tpt) REVERT: A 487 GLU cc_start: 0.8309 (pm20) cc_final: 0.7949 (pm20) REVERT: A 490 PHE cc_start: 0.8336 (m-80) cc_final: 0.8006 (m-80) REVERT: A 509 TYR cc_start: 0.7677 (p90) cc_final: 0.7314 (p90) REVERT: A 510 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6554 (mm-30) REVERT: B 109 LYS cc_start: 0.8755 (mmtm) cc_final: 0.8430 (mptt) REVERT: B 128 ARG cc_start: 0.9066 (mmm-85) cc_final: 0.8766 (mmt90) REVERT: B 161 ARG cc_start: 0.9428 (mpp-170) cc_final: 0.9161 (mpt180) REVERT: B 165 PHE cc_start: 0.7868 (p90) cc_final: 0.7130 (p90) REVERT: B 186 VAL cc_start: 0.9343 (OUTLIER) cc_final: 0.8997 (m) REVERT: B 206 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8191 (ttpt) REVERT: B 216 ASP cc_start: 0.8989 (t70) cc_final: 0.8633 (t0) REVERT: B 243 GLN cc_start: 0.8671 (mp10) cc_final: 0.8441 (mp-120) REVERT: B 258 TYR cc_start: 0.7954 (t80) cc_final: 0.7735 (t80) REVERT: B 261 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8297 (p0) REVERT: B 283 GLN cc_start: 0.8702 (tt0) cc_final: 0.8408 (mt0) REVERT: B 311 LYS cc_start: 0.8846 (tmtt) cc_final: 0.7875 (tppt) REVERT: B 337 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7251 (tt) REVERT: B 386 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8513 (pmm) REVERT: B 407 ARG cc_start: 0.7514 (ttt180) cc_final: 0.7239 (ttt90) REVERT: B 408 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8671 (mp) REVERT: B 420 MET cc_start: 0.6910 (mmm) cc_final: 0.6416 (mmm) REVERT: B 469 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.7742 (pt0) REVERT: B 470 ASP cc_start: 0.8669 (m-30) cc_final: 0.8248 (m-30) REVERT: B 482 MET cc_start: 0.8726 (tpt) cc_final: 0.8398 (tpt) REVERT: B 487 GLU cc_start: 0.8385 (pm20) cc_final: 0.8088 (pm20) REVERT: B 490 PHE cc_start: 0.8347 (m-80) cc_final: 0.8103 (m-80) REVERT: B 509 TYR cc_start: 0.7632 (p90) cc_final: 0.7264 (p90) REVERT: C 109 LYS cc_start: 0.8807 (mmtm) cc_final: 0.8494 (mptt) REVERT: C 111 GLU cc_start: 0.8562 (mp0) cc_final: 0.7944 (pm20) REVERT: C 132 GLU cc_start: 0.9441 (mp0) cc_final: 0.9140 (mp0) REVERT: C 165 PHE cc_start: 0.8066 (p90) cc_final: 0.7856 (p90) REVERT: C 199 GLU cc_start: 0.9493 (tp30) cc_final: 0.9265 (tp30) REVERT: C 203 ARG cc_start: 0.9340 (ptp-110) cc_final: 0.9123 (ptp-110) REVERT: C 206 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8089 (ttpt) REVERT: C 208 LYS cc_start: 0.8667 (mtpp) cc_final: 0.8012 (mtpp) REVERT: C 250 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7532 (pp) REVERT: C 297 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8718 (tm) REVERT: C 311 LYS cc_start: 0.8753 (tmtt) cc_final: 0.7839 (tppt) REVERT: C 313 LEU cc_start: 0.9333 (mp) cc_final: 0.9088 (mp) REVERT: C 337 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7174 (tt) REVERT: C 348 TYR cc_start: 0.9244 (t80) cc_final: 0.8969 (t80) REVERT: C 352 GLU cc_start: 0.8646 (tp30) cc_final: 0.8245 (tp30) REVERT: C 386 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8243 (pmm) REVERT: C 420 MET cc_start: 0.6740 (mmm) cc_final: 0.6361 (mmm) REVERT: C 470 ASP cc_start: 0.8557 (m-30) cc_final: 0.8281 (m-30) REVERT: C 482 MET cc_start: 0.8620 (tpt) cc_final: 0.8396 (tpt) REVERT: C 487 GLU cc_start: 0.8393 (pm20) cc_final: 0.7984 (pm20) REVERT: C 490 PHE cc_start: 0.8351 (m-80) cc_final: 0.8094 (m-80) REVERT: C 509 TYR cc_start: 0.7752 (p90) cc_final: 0.7410 (p90) REVERT: C 510 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6740 (mm-30) REVERT: D 32 TYR cc_start: 0.8421 (m-10) cc_final: 0.8150 (m-10) REVERT: D 161 ARG cc_start: 0.9515 (mpp-170) cc_final: 0.9224 (mpt-90) REVERT: D 165 PHE cc_start: 0.7936 (p90) cc_final: 0.7720 (p90) REVERT: D 166 LEU cc_start: 0.8233 (tp) cc_final: 0.7987 (tp) REVERT: D 199 GLU cc_start: 0.9427 (tp30) cc_final: 0.8783 (tp30) REVERT: D 203 ARG cc_start: 0.9365 (ptp-110) cc_final: 0.8714 (mtm-85) REVERT: D 216 ASP cc_start: 0.9023 (t70) cc_final: 0.8674 (t0) REVERT: D 261 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.8282 (p0) REVERT: D 265 GLN cc_start: 0.9257 (mm110) cc_final: 0.9031 (mm-40) REVERT: D 297 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8809 (tm) REVERT: D 309 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8819 (pt0) REVERT: D 311 LYS cc_start: 0.8771 (tmtt) cc_final: 0.7869 (tppt) REVERT: D 313 LEU cc_start: 0.9343 (mp) cc_final: 0.9137 (mp) REVERT: D 337 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7301 (tt) REVERT: D 386 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8332 (ppp) REVERT: D 400 TYR cc_start: 0.7801 (m-80) cc_final: 0.7458 (m-80) REVERT: D 407 ARG cc_start: 0.7303 (ttt180) cc_final: 0.6667 (ttt180) REVERT: D 420 MET cc_start: 0.6765 (mmm) cc_final: 0.6434 (mmm) REVERT: D 469 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.7791 (pt0) REVERT: D 470 ASP cc_start: 0.8750 (m-30) cc_final: 0.8354 (m-30) REVERT: D 482 MET cc_start: 0.8681 (tpt) cc_final: 0.8427 (tpt) REVERT: D 484 TYR cc_start: 0.9006 (m-80) cc_final: 0.8624 (m-10) REVERT: D 487 GLU cc_start: 0.8431 (pm20) cc_final: 0.8035 (pm20) REVERT: D 488 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7639 (tp) REVERT: D 490 PHE cc_start: 0.8321 (m-80) cc_final: 0.7964 (m-80) REVERT: D 509 TYR cc_start: 0.7589 (p90) cc_final: 0.7191 (p90) REVERT: D 510 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6843 (mm-30) REVERT: E 62 LYS cc_start: 0.9155 (mmtp) cc_final: 0.8865 (mttm) REVERT: E 78 MET cc_start: 0.8062 (ttm) cc_final: 0.7672 (ttt) REVERT: E 109 LYS cc_start: 0.8832 (mmtm) cc_final: 0.8533 (mptt) REVERT: E 128 ARG cc_start: 0.9107 (mmm-85) cc_final: 0.8770 (mmt90) REVERT: E 132 GLU cc_start: 0.9457 (mp0) cc_final: 0.9162 (mp0) REVERT: E 165 PHE cc_start: 0.8074 (p90) cc_final: 0.7855 (p90) REVERT: E 166 LEU cc_start: 0.8158 (tp) cc_final: 0.7885 (tp) REVERT: E 185 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7596 (mt) REVERT: E 199 GLU cc_start: 0.9482 (tp30) cc_final: 0.8815 (tp30) REVERT: E 202 GLN cc_start: 0.9289 (mm-40) cc_final: 0.8136 (pp30) REVERT: E 206 LYS cc_start: 0.8275 (tppt) cc_final: 0.7900 (tppt) REVERT: E 216 ASP cc_start: 0.9130 (t70) cc_final: 0.8782 (t0) REVERT: E 250 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7451 (pp) REVERT: E 297 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8668 (tm) REVERT: E 311 LYS cc_start: 0.8807 (tmtt) cc_final: 0.7885 (tppt) REVERT: E 337 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7160 (tt) REVERT: E 348 TYR cc_start: 0.9262 (t80) cc_final: 0.8818 (t80) REVERT: E 386 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8280 (ppp) REVERT: E 400 TYR cc_start: 0.7553 (m-80) cc_final: 0.7347 (m-80) REVERT: E 407 ARG cc_start: 0.7346 (ttt180) cc_final: 0.6794 (tpt-90) REVERT: E 408 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8464 (mp) REVERT: E 420 MET cc_start: 0.6849 (mmm) cc_final: 0.6528 (mmm) REVERT: E 465 GLN cc_start: 0.7983 (pt0) cc_final: 0.7610 (mt0) REVERT: E 469 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7693 (pt0) REVERT: E 470 ASP cc_start: 0.8731 (m-30) cc_final: 0.8422 (m-30) REVERT: E 482 MET cc_start: 0.8595 (tpt) cc_final: 0.8381 (tpt) REVERT: E 487 GLU cc_start: 0.8463 (pm20) cc_final: 0.8144 (pm20) REVERT: E 490 PHE cc_start: 0.8386 (m-80) cc_final: 0.8074 (m-80) REVERT: E 509 TYR cc_start: 0.7886 (p90) cc_final: 0.7509 (p90) REVERT: E 510 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6593 (mm-30) REVERT: F 32 TYR cc_start: 0.8318 (m-10) cc_final: 0.8039 (m-10) REVERT: F 62 LYS cc_start: 0.9249 (mmtp) cc_final: 0.8753 (mttm) REVERT: F 65 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9044 (pt) REVERT: F 78 MET cc_start: 0.8296 (ttm) cc_final: 0.7932 (ttt) REVERT: F 109 LYS cc_start: 0.8569 (mmtm) cc_final: 0.8226 (mppt) REVERT: F 132 GLU cc_start: 0.9482 (mp0) cc_final: 0.9215 (mp0) REVERT: F 165 PHE cc_start: 0.8292 (p90) cc_final: 0.7859 (p90) REVERT: F 166 LEU cc_start: 0.8166 (tp) cc_final: 0.7870 (tp) REVERT: F 199 GLU cc_start: 0.9470 (tp30) cc_final: 0.9216 (tp30) REVERT: F 206 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8130 (ttpt) REVERT: F 216 ASP cc_start: 0.9072 (t70) cc_final: 0.8726 (t0) REVERT: F 235 LEU cc_start: 0.9006 (mt) cc_final: 0.8379 (mt) REVERT: F 261 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8282 (p0) REVERT: F 262 LEU cc_start: 0.9228 (tp) cc_final: 0.9012 (tp) REVERT: F 283 GLN cc_start: 0.8642 (tt0) cc_final: 0.8360 (mt0) REVERT: F 297 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8789 (tm) REVERT: F 311 LYS cc_start: 0.8782 (tmtt) cc_final: 0.7875 (tppt) REVERT: F 337 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7277 (tt) REVERT: F 386 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8400 (ppp) REVERT: F 407 ARG cc_start: 0.7622 (ttt180) cc_final: 0.7271 (ttt90) REVERT: F 408 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8586 (mp) REVERT: F 469 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.7755 (pt0) REVERT: F 470 ASP cc_start: 0.8668 (m-30) cc_final: 0.8308 (m-30) REVERT: F 482 MET cc_start: 0.8701 (tpt) cc_final: 0.8478 (tpt) REVERT: F 487 GLU cc_start: 0.8561 (pm20) cc_final: 0.8245 (pm20) REVERT: F 490 PHE cc_start: 0.8447 (m-80) cc_final: 0.8113 (m-80) REVERT: F 509 TYR cc_start: 0.7856 (p90) cc_final: 0.7643 (p90) REVERT: F 510 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6727 (mm-30) REVERT: G 32 TYR cc_start: 0.8518 (m-80) cc_final: 0.8262 (m-10) REVERT: G 109 LYS cc_start: 0.8847 (mmtm) cc_final: 0.8563 (mptt) REVERT: G 132 GLU cc_start: 0.9453 (mp0) cc_final: 0.9143 (mp0) REVERT: G 165 PHE cc_start: 0.8063 (p90) cc_final: 0.7796 (p90) REVERT: G 166 LEU cc_start: 0.8160 (tp) cc_final: 0.7892 (tp) REVERT: G 179 MET cc_start: 0.7312 (ptm) cc_final: 0.7111 (ptt) REVERT: G 199 GLU cc_start: 0.9459 (tp30) cc_final: 0.9126 (tp30) REVERT: G 206 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8088 (ttpt) REVERT: G 208 LYS cc_start: 0.8001 (ttmm) cc_final: 0.7674 (ttmm) REVERT: G 289 TYR cc_start: 0.8872 (t80) cc_final: 0.8512 (t80) REVERT: G 297 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8691 (tm) REVERT: G 311 LYS cc_start: 0.8728 (tmtt) cc_final: 0.7873 (tppt) REVERT: G 337 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7250 (tt) REVERT: G 386 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8454 (pmm) REVERT: G 407 ARG cc_start: 0.7394 (ttt180) cc_final: 0.6888 (tpt-90) REVERT: G 408 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8476 (mp) REVERT: G 420 MET cc_start: 0.6710 (mmm) cc_final: 0.6362 (mmm) REVERT: G 470 ASP cc_start: 0.8672 (m-30) cc_final: 0.8385 (m-30) REVERT: G 482 MET cc_start: 0.8726 (tpt) cc_final: 0.8501 (tpt) REVERT: G 487 GLU cc_start: 0.8518 (pm20) cc_final: 0.8137 (pm20) REVERT: G 489 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7990 (tttt) REVERT: G 490 PHE cc_start: 0.8398 (m-80) cc_final: 0.8056 (m-80) REVERT: G 509 TYR cc_start: 0.7970 (p90) cc_final: 0.7578 (p90) REVERT: H 62 LYS cc_start: 0.9236 (mmtp) cc_final: 0.8786 (mttm) REVERT: H 78 MET cc_start: 0.7672 (ttt) cc_final: 0.7345 (ttt) REVERT: H 109 LYS cc_start: 0.8772 (mmtm) cc_final: 0.8436 (mptt) REVERT: H 161 ARG cc_start: 0.9584 (mpp-170) cc_final: 0.9175 (mpt-90) REVERT: H 165 PHE cc_start: 0.7957 (p90) cc_final: 0.7730 (p90) REVERT: H 199 GLU cc_start: 0.9436 (tp30) cc_final: 0.9233 (tp30) REVERT: H 206 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8011 (ttpt) REVERT: H 216 ASP cc_start: 0.8963 (t70) cc_final: 0.8641 (t0) REVERT: H 235 LEU cc_start: 0.9008 (mt) cc_final: 0.8348 (mt) REVERT: H 262 LEU cc_start: 0.9166 (tp) cc_final: 0.8965 (tp) REVERT: H 297 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8724 (tm) REVERT: H 311 LYS cc_start: 0.8766 (tmtt) cc_final: 0.7832 (tppt) REVERT: H 337 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7201 (tt) REVERT: H 348 TYR cc_start: 0.9028 (t80) cc_final: 0.8730 (t80) REVERT: H 386 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8159 (pmm) REVERT: H 401 PHE cc_start: 0.8143 (p90) cc_final: 0.7922 (p90) REVERT: H 469 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7526 (pt0) REVERT: H 470 ASP cc_start: 0.8765 (m-30) cc_final: 0.8386 (m-30) REVERT: H 482 MET cc_start: 0.8684 (tpt) cc_final: 0.8419 (tpt) REVERT: H 487 GLU cc_start: 0.8427 (pm20) cc_final: 0.8006 (pm20) REVERT: H 490 PHE cc_start: 0.8361 (m-80) cc_final: 0.7905 (m-80) REVERT: H 509 TYR cc_start: 0.8035 (p90) cc_final: 0.7751 (p90) outliers start: 262 outliers final: 165 residues processed: 1212 average time/residue: 0.1842 time to fit residues: 360.8608 Evaluate side-chains 1209 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 991 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 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 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 386 MET Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain 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 186 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 294 TYR 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 314 ILE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 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 261 ASP Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 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 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 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 337 LEU Chi-restraints excluded: chain E residue 361 VAL 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 408 LEU Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 186 VAL 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 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 304 VAL Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain G residue 489 LYS 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 268 VAL Chi-restraints excluded: chain H residue 294 TYR 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 379 LEU Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 469 GLN Chi-restraints excluded: chain H residue 494 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 374 optimal weight: 4.9990 chunk 362 optimal weight: 0.9990 chunk 269 optimal weight: 6.9990 chunk 225 optimal weight: 1.9990 chunk 358 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 274 optimal weight: 0.6980 chunk 250 optimal weight: 0.1980 chunk 219 optimal weight: 0.8980 chunk 350 optimal weight: 20.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 198 ASN A 253 HIS ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 GLN ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.168400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.131580 restraints weight = 51249.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.137226 restraints weight = 29710.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.141175 restraints weight = 20196.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.143935 restraints weight = 15104.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.146020 restraints weight = 12104.052| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31592 Z= 0.142 Angle : 0.843 11.969 42888 Z= 0.393 Chirality : 0.049 0.217 4888 Planarity : 0.005 0.055 5328 Dihedral : 13.741 143.349 4685 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 7.93 % Allowed : 29.92 % Favored : 62.16 % 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: -2.23 (0.13), residues: 3880 helix: -1.39 (0.14), residues: 1216 sheet: -2.28 (0.19), residues: 576 loop : -1.19 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 161 TYR 0.023 0.002 TYR D 233 PHE 0.018 0.001 PHE G 90 HIS 0.007 0.001 HIS F 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (31576) covalent geometry : angle 0.84281 / 0.39 (42888) hydrogen bonds : bond 0.03454 / 2.25 ( 832) hydrogen bonds : angle 5.29308 / 3.68 ( 2376) Misc. bond : bond 0.00040 / 0.02 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1288 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 253 poor density : 1035 time to evaluate : 1.112 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: A 32 TYR cc_start: 0.8604 (m-10) cc_final: 0.8382 (m-10) REVERT: A 51 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8009 (pp) REVERT: A 109 LYS cc_start: 0.8883 (mmtm) cc_final: 0.8580 (mppt) REVERT: A 128 ARG cc_start: 0.8827 (mmt90) cc_final: 0.8597 (mmt90) REVERT: A 216 ASP cc_start: 0.8997 (t70) cc_final: 0.8662 (t0) REVERT: A 250 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7697 (pp) REVERT: A 297 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8673 (tm) REVERT: A 311 LYS cc_start: 0.8705 (tmtt) cc_final: 0.8280 (tmtt) REVERT: A 337 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7130 (tt) REVERT: A 348 TYR cc_start: 0.9003 (t80) cc_final: 0.8784 (t80) REVERT: A 352 GLU cc_start: 0.8779 (tp30) cc_final: 0.8303 (tp30) REVERT: A 386 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8336 (pmm) REVERT: A 420 MET cc_start: 0.6667 (mmm) cc_final: 0.6304 (mmm) REVERT: A 469 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7587 (pt0) REVERT: A 470 ASP cc_start: 0.8658 (m-30) cc_final: 0.8322 (m-30) REVERT: A 482 MET cc_start: 0.8682 (tpt) cc_final: 0.8402 (tpt) REVERT: A 484 TYR cc_start: 0.9095 (m-80) cc_final: 0.8645 (m-80) REVERT: A 487 GLU cc_start: 0.8226 (pm20) cc_final: 0.7797 (pm20) REVERT: A 490 PHE cc_start: 0.8412 (m-80) cc_final: 0.8091 (m-80) REVERT: A 509 TYR cc_start: 0.7715 (p90) cc_final: 0.7441 (p90) REVERT: A 510 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6564 (mm-30) REVERT: B 32 TYR cc_start: 0.8325 (m-10) cc_final: 0.8049 (m-10) REVERT: B 109 LYS cc_start: 0.8778 (mmtm) cc_final: 0.8473 (mptt) REVERT: B 128 ARG cc_start: 0.9024 (mmm-85) cc_final: 0.8773 (mmt90) REVERT: B 165 PHE cc_start: 0.7934 (p90) cc_final: 0.7697 (p90) REVERT: B 186 VAL cc_start: 0.9359 (OUTLIER) cc_final: 0.9006 (m) REVERT: B 203 ARG cc_start: 0.9282 (ptp-110) cc_final: 0.9040 (ptp-110) REVERT: B 206 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8200 (ttpt) REVERT: B 216 ASP cc_start: 0.8999 (t70) cc_final: 0.8644 (t0) REVERT: B 243 GLN cc_start: 0.8739 (mp10) cc_final: 0.8506 (mp-120) REVERT: B 258 TYR cc_start: 0.7911 (t80) cc_final: 0.7693 (t80) REVERT: B 261 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8347 (p0) REVERT: B 265 GLN cc_start: 0.9288 (mm110) cc_final: 0.9042 (mm-40) REVERT: B 311 LYS cc_start: 0.8709 (tmtt) cc_final: 0.7811 (tppt) REVERT: B 337 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7266 (tt) REVERT: B 386 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8326 (pmm) REVERT: B 407 ARG cc_start: 0.7505 (ttt180) cc_final: 0.7201 (ttt90) REVERT: B 420 MET cc_start: 0.7266 (mmm) cc_final: 0.6713 (mmm) REVERT: B 470 ASP cc_start: 0.8726 (m-30) cc_final: 0.8347 (m-30) REVERT: B 482 MET cc_start: 0.8736 (tpt) cc_final: 0.8461 (tpt) REVERT: B 487 GLU cc_start: 0.8306 (pm20) cc_final: 0.7914 (pm20) REVERT: B 509 TYR cc_start: 0.7722 (p90) cc_final: 0.7419 (p90) REVERT: C 109 LYS cc_start: 0.8814 (mmtm) cc_final: 0.8527 (mptt) REVERT: C 132 GLU cc_start: 0.9427 (mp0) cc_final: 0.9106 (mp0) REVERT: C 165 PHE cc_start: 0.8087 (p90) cc_final: 0.7853 (p90) REVERT: C 199 GLU cc_start: 0.9505 (tp30) cc_final: 0.9287 (tp30) REVERT: C 206 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8162 (ttpt) REVERT: C 208 LYS cc_start: 0.8673 (mtpp) cc_final: 0.8472 (mtpp) REVERT: C 216 ASP cc_start: 0.9104 (t70) cc_final: 0.8731 (t0) REVERT: C 250 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7639 (pp) REVERT: C 265 GLN cc_start: 0.9236 (mm110) cc_final: 0.8973 (mm-40) REVERT: C 297 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8728 (tm) REVERT: C 311 LYS cc_start: 0.8701 (tmtt) cc_final: 0.7768 (tppt) REVERT: C 313 LEU cc_start: 0.9340 (mp) cc_final: 0.9129 (mp) REVERT: C 337 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7224 (tt) REVERT: C 352 GLU cc_start: 0.8629 (tp30) cc_final: 0.8337 (tp30) REVERT: C 386 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8348 (ppp) REVERT: C 420 MET cc_start: 0.6790 (mmm) cc_final: 0.6392 (mmm) REVERT: C 470 ASP cc_start: 0.8629 (m-30) cc_final: 0.8305 (m-30) REVERT: C 490 PHE cc_start: 0.8339 (m-80) cc_final: 0.8057 (m-80) REVERT: C 509 TYR cc_start: 0.7777 (p90) cc_final: 0.7544 (p90) REVERT: C 510 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6774 (mm-30) REVERT: D 32 TYR cc_start: 0.8508 (m-10) cc_final: 0.8296 (m-10) REVERT: D 109 LYS cc_start: 0.8631 (mmtm) cc_final: 0.8177 (mptt) REVERT: D 161 ARG cc_start: 0.9527 (mpp-170) cc_final: 0.9168 (mpt-90) REVERT: D 165 PHE cc_start: 0.7962 (p90) cc_final: 0.7711 (p90) REVERT: D 199 GLU cc_start: 0.9437 (tp30) cc_final: 0.8772 (tp30) REVERT: D 203 ARG cc_start: 0.9370 (ptp-110) cc_final: 0.9049 (ptp-110) REVERT: D 206 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8153 (ttpt) REVERT: D 216 ASP cc_start: 0.9046 (t70) cc_final: 0.8697 (t0) REVERT: D 265 GLN cc_start: 0.9250 (mm110) cc_final: 0.8973 (mm-40) REVERT: D 297 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8816 (tm) REVERT: D 309 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8837 (pt0) REVERT: D 311 LYS cc_start: 0.8697 (tmtt) cc_final: 0.7783 (tppt) REVERT: D 337 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7323 (tt) REVERT: D 386 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8254 (ppp) REVERT: D 400 TYR cc_start: 0.7703 (m-80) cc_final: 0.7298 (m-80) REVERT: D 407 ARG cc_start: 0.7283 (ttt180) cc_final: 0.6608 (ttt180) REVERT: D 420 MET cc_start: 0.6872 (mmm) cc_final: 0.6557 (mmm) REVERT: D 464 ILE cc_start: 0.8805 (pp) cc_final: 0.8599 (pp) REVERT: D 469 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.7593 (pt0) REVERT: D 470 ASP cc_start: 0.8710 (m-30) cc_final: 0.8330 (m-30) REVERT: D 488 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7554 (tp) REVERT: D 490 PHE cc_start: 0.8369 (m-80) cc_final: 0.7972 (m-80) REVERT: D 509 TYR cc_start: 0.7593 (p90) cc_final: 0.7258 (p90) REVERT: D 510 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6817 (mm-30) REVERT: E 32 TYR cc_start: 0.8584 (m-10) cc_final: 0.8246 (m-10) REVERT: E 62 LYS cc_start: 0.9138 (mmtp) cc_final: 0.8853 (mttm) REVERT: E 78 MET cc_start: 0.8166 (ttm) cc_final: 0.7748 (ttt) REVERT: E 109 LYS cc_start: 0.8868 (mmtm) cc_final: 0.8574 (mptt) REVERT: E 128 ARG cc_start: 0.9107 (mmm-85) cc_final: 0.8844 (mmm-85) REVERT: E 132 GLU cc_start: 0.9459 (mp0) cc_final: 0.9134 (mp0) REVERT: E 165 PHE cc_start: 0.8091 (p90) cc_final: 0.7883 (p90) REVERT: E 185 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7606 (mt) REVERT: E 206 LYS cc_start: 0.8298 (tppt) cc_final: 0.7924 (tppt) REVERT: E 216 ASP cc_start: 0.9138 (t70) cc_final: 0.8787 (t0) REVERT: E 250 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7578 (pp) REVERT: E 297 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8678 (tm) REVERT: E 311 LYS cc_start: 0.8732 (tmtt) cc_final: 0.8314 (tmtt) REVERT: E 337 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7142 (tt) REVERT: E 348 TYR cc_start: 0.9109 (t80) cc_final: 0.8830 (t80) REVERT: E 386 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8350 (ppp) REVERT: E 407 ARG cc_start: 0.7330 (ttt180) cc_final: 0.7066 (ttt180) REVERT: E 408 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8605 (mp) REVERT: E 420 MET cc_start: 0.6854 (mmm) cc_final: 0.6518 (mmm) REVERT: E 465 GLN cc_start: 0.7874 (pt0) cc_final: 0.7669 (tt0) REVERT: E 469 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7658 (pt0) REVERT: E 470 ASP cc_start: 0.8744 (m-30) cc_final: 0.8301 (m-30) REVERT: E 490 PHE cc_start: 0.8402 (m-80) cc_final: 0.8199 (m-80) REVERT: E 509 TYR cc_start: 0.7911 (p90) cc_final: 0.7605 (p90) REVERT: E 510 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6635 (mm-30) REVERT: F 32 TYR cc_start: 0.8431 (m-10) cc_final: 0.8159 (m-10) REVERT: F 62 LYS cc_start: 0.9279 (mmtp) cc_final: 0.9022 (mttm) REVERT: F 65 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9078 (pt) REVERT: F 66 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8014 (p) REVERT: F 78 MET cc_start: 0.8066 (ttm) cc_final: 0.7702 (ttt) REVERT: F 109 LYS cc_start: 0.8658 (mmtm) cc_final: 0.8291 (mptt) REVERT: F 132 GLU cc_start: 0.9475 (mp0) cc_final: 0.9188 (mp0) REVERT: F 157 ILE cc_start: 0.9283 (tt) cc_final: 0.9055 (tt) REVERT: F 165 PHE cc_start: 0.8247 (p90) cc_final: 0.7922 (p90) REVERT: F 166 LEU cc_start: 0.8212 (tp) cc_final: 0.7909 (tp) REVERT: F 199 GLU cc_start: 0.9458 (tp30) cc_final: 0.9116 (tp30) REVERT: F 203 ARG cc_start: 0.9333 (ptp-110) cc_final: 0.9048 (ptp-110) REVERT: F 206 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8155 (ttpt) REVERT: F 216 ASP cc_start: 0.9098 (t70) cc_final: 0.8740 (t0) REVERT: F 261 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8320 (p0) REVERT: F 262 LEU cc_start: 0.9215 (tp) cc_final: 0.9008 (tp) REVERT: F 297 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8777 (tm) REVERT: F 311 LYS cc_start: 0.8717 (tmtt) cc_final: 0.7843 (tppt) REVERT: F 337 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7259 (tt) REVERT: F 386 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8227 (pmm) REVERT: F 407 ARG cc_start: 0.7611 (ttt180) cc_final: 0.7210 (ttt90) REVERT: F 408 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8578 (mp) REVERT: F 469 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.7597 (pt0) REVERT: F 470 ASP cc_start: 0.8707 (m-30) cc_final: 0.8357 (m-30) REVERT: F 482 MET cc_start: 0.8784 (tpt) cc_final: 0.8535 (tpt) REVERT: F 487 GLU cc_start: 0.8432 (pm20) cc_final: 0.8025 (pm20) REVERT: F 490 PHE cc_start: 0.8464 (m-80) cc_final: 0.8204 (m-80) REVERT: F 509 TYR cc_start: 0.7872 (p90) cc_final: 0.7604 (p90) REVERT: F 510 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6447 (mm-30) REVERT: G 32 TYR cc_start: 0.8584 (m-80) cc_final: 0.8285 (m-10) REVERT: G 78 MET cc_start: 0.7323 (ttt) cc_final: 0.7059 (tmm) REVERT: G 109 LYS cc_start: 0.8852 (mmtm) cc_final: 0.8629 (mptt) REVERT: G 128 ARG cc_start: 0.8837 (mmt90) cc_final: 0.8447 (mmt90) REVERT: G 132 GLU cc_start: 0.9439 (mp0) cc_final: 0.9123 (mp0) REVERT: G 199 GLU cc_start: 0.9477 (tp30) cc_final: 0.9246 (tp30) REVERT: G 206 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8135 (ttpt) REVERT: G 208 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7647 (ttmm) REVERT: G 297 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8637 (tm) REVERT: G 311 LYS cc_start: 0.8737 (tmtt) cc_final: 0.8330 (tmtt) REVERT: G 337 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7162 (tt) REVERT: G 361 VAL cc_start: 0.9367 (OUTLIER) cc_final: 0.9166 (m) REVERT: G 386 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8372 (pmm) REVERT: G 408 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8617 (mp) REVERT: G 420 MET cc_start: 0.6682 (mmm) cc_final: 0.6328 (mmm) REVERT: G 470 ASP cc_start: 0.8656 (m-30) cc_final: 0.8394 (m-30) REVERT: G 482 MET cc_start: 0.8728 (tpt) cc_final: 0.8457 (tpt) REVERT: G 487 GLU cc_start: 0.8466 (pm20) cc_final: 0.8059 (pm20) REVERT: G 489 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.8029 (tttt) REVERT: G 490 PHE cc_start: 0.8476 (m-80) cc_final: 0.8092 (m-80) REVERT: G 509 TYR cc_start: 0.7914 (p90) cc_final: 0.7587 (p90) REVERT: H 62 LYS cc_start: 0.9273 (mmtp) cc_final: 0.8828 (mttm) REVERT: H 78 MET cc_start: 0.7535 (ttt) cc_final: 0.7170 (ttt) REVERT: H 109 LYS cc_start: 0.8717 (mmtm) cc_final: 0.8490 (mptt) REVERT: H 161 ARG cc_start: 0.9595 (mpp-170) cc_final: 0.9230 (mpt-90) REVERT: H 165 PHE cc_start: 0.8047 (p90) cc_final: 0.7769 (p90) REVERT: H 199 GLU cc_start: 0.9496 (tp30) cc_final: 0.9260 (tp30) REVERT: H 206 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8010 (ttpt) REVERT: H 216 ASP cc_start: 0.9012 (t70) cc_final: 0.8671 (t0) REVERT: H 235 LEU cc_start: 0.9053 (mt) cc_final: 0.8434 (mt) REVERT: H 250 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7801 (pp) REVERT: H 277 GLN cc_start: 0.9235 (tm-30) cc_final: 0.9007 (tm-30) REVERT: H 283 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8413 (mt0) REVERT: H 297 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8752 (tm) REVERT: H 311 LYS cc_start: 0.8679 (tmtt) cc_final: 0.7822 (tppt) REVERT: H 337 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7241 (tt) REVERT: H 348 TYR cc_start: 0.8866 (t80) cc_final: 0.8663 (t80) REVERT: H 386 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8107 (pmm) REVERT: H 401 PHE cc_start: 0.8105 (p90) cc_final: 0.7888 (p90) REVERT: H 469 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7521 (pt0) REVERT: H 470 ASP cc_start: 0.8742 (m-30) cc_final: 0.8358 (m-30) REVERT: H 482 MET cc_start: 0.8796 (tpt) cc_final: 0.8525 (tpt) REVERT: H 487 GLU cc_start: 0.8363 (pm20) cc_final: 0.7968 (pm20) REVERT: H 490 PHE cc_start: 0.8436 (m-80) cc_final: 0.8054 (m-80) REVERT: H 509 TYR cc_start: 0.8054 (p90) cc_final: 0.7834 (p90) outliers start: 253 outliers final: 158 residues processed: 1159 average time/residue: 0.1855 time to fit residues: 348.6818 Evaluate side-chains 1177 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 963 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 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 336 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 261 ASP 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 314 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 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 186 VAL 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 284 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 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 314 ILE Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 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 120 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 186 VAL 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 304 VAL Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 222 ILE Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 294 TYR 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 370 VAL Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 469 GLN Chi-restraints excluded: chain H residue 494 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 15 optimal weight: 9.9990 chunk 363 optimal weight: 0.9990 chunk 156 optimal weight: 7.9990 chunk 376 optimal weight: 0.8980 chunk 272 optimal weight: 1.9990 chunk 312 optimal weight: 9.9990 chunk 264 optimal weight: 10.0000 chunk 254 optimal weight: 10.0000 chunk 163 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 HIS ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 GLN ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 GLN ** F 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 253 HIS G 303 ASN G 465 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.167177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.130318 restraints weight = 51653.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.135815 restraints weight = 30384.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.139725 restraints weight = 20901.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.142527 restraints weight = 15732.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.144507 restraints weight = 12626.023| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31592 Z= 0.154 Angle : 0.854 11.326 42888 Z= 0.401 Chirality : 0.049 0.213 4888 Planarity : 0.005 0.085 5328 Dihedral : 13.266 140.469 4675 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 8.33 % Allowed : 30.83 % Favored : 60.84 % 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: -2.16 (0.13), residues: 3880 helix: -1.35 (0.14), residues: 1216 sheet: -2.23 (0.19), residues: 576 loop : -1.15 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 231 TYR 0.024 0.002 TYR D 484 PHE 0.017 0.001 PHE C 90 HIS 0.008 0.001 HIS B 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (31576) covalent geometry : angle 0.85441 / 0.40 (42888) hydrogen bonds : bond 0.03478 / 2.27 ( 832) hydrogen bonds : angle 5.27884 / 3.65 ( 2376) Misc. bond : bond 0.00034 / 0.02 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1289 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 266 poor density : 1023 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7961 (pp) REVERT: A 74 THR cc_start: 0.8069 (OUTLIER) cc_final: 0.7617 (p) REVERT: A 109 LYS cc_start: 0.8918 (mmtm) cc_final: 0.8655 (mppt) REVERT: A 186 VAL cc_start: 0.9378 (m) cc_final: 0.9064 (m) REVERT: A 202 GLN cc_start: 0.9343 (mt0) cc_final: 0.8901 (mt0) REVERT: A 206 LYS cc_start: 0.8441 (mtmt) cc_final: 0.7890 (ttpt) REVERT: A 250 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7819 (pp) REVERT: A 261 ASP cc_start: 0.9002 (t0) cc_final: 0.8791 (m-30) REVERT: A 285 ASN cc_start: 0.9498 (m110) cc_final: 0.9173 (m110) REVERT: A 311 LYS cc_start: 0.8678 (tmtt) cc_final: 0.8240 (tmtt) REVERT: A 337 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7143 (tt) REVERT: A 386 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8416 (pmm) REVERT: A 420 MET cc_start: 0.6738 (mmm) cc_final: 0.6356 (mmm) REVERT: A 470 ASP cc_start: 0.8595 (m-30) cc_final: 0.8325 (m-30) REVERT: A 490 PHE cc_start: 0.8420 (m-80) cc_final: 0.8182 (m-80) REVERT: A 509 TYR cc_start: 0.7741 (p90) cc_final: 0.7518 (p90) REVERT: A 510 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6595 (mm-30) REVERT: B 32 TYR cc_start: 0.8434 (m-10) cc_final: 0.8196 (m-10) REVERT: B 109 LYS cc_start: 0.8739 (mmtm) cc_final: 0.8496 (mptt) REVERT: B 165 PHE cc_start: 0.7962 (p90) cc_final: 0.7699 (p90) REVERT: B 186 VAL cc_start: 0.9347 (OUTLIER) cc_final: 0.8891 (m) REVERT: B 202 GLN cc_start: 0.9342 (mm-40) cc_final: 0.8997 (mm-40) REVERT: B 203 ARG cc_start: 0.9296 (ptp-110) cc_final: 0.9065 (ptp-110) REVERT: B 206 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8131 (ttpt) REVERT: B 216 ASP cc_start: 0.8988 (t70) cc_final: 0.8626 (t0) REVERT: B 250 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7641 (pp) REVERT: B 258 TYR cc_start: 0.7891 (t80) cc_final: 0.7622 (t80) REVERT: B 265 GLN cc_start: 0.9275 (mm110) cc_final: 0.9000 (mm-40) REVERT: B 311 LYS cc_start: 0.8737 (tmtt) cc_final: 0.7751 (tppt) REVERT: B 337 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7190 (tt) REVERT: B 386 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8163 (pmm) REVERT: B 407 ARG cc_start: 0.7536 (ttt180) cc_final: 0.7170 (ttt90) REVERT: B 408 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8532 (mp) REVERT: B 420 MET cc_start: 0.7396 (mmm) cc_final: 0.6775 (mmm) REVERT: B 469 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.7531 (pt0) REVERT: B 470 ASP cc_start: 0.8740 (m-30) cc_final: 0.8342 (m-30) REVERT: B 490 PHE cc_start: 0.8448 (m-80) cc_final: 0.8184 (m-80) REVERT: B 509 TYR cc_start: 0.7801 (p90) cc_final: 0.7581 (p90) REVERT: C 78 MET cc_start: 0.7327 (ttt) cc_final: 0.6748 (tmm) REVERT: C 111 GLU cc_start: 0.8195 (mp0) cc_final: 0.7328 (pm20) REVERT: C 128 ARG cc_start: 0.9010 (mmm-85) cc_final: 0.8667 (mmt90) REVERT: C 129 ASP cc_start: 0.9026 (m-30) cc_final: 0.8820 (m-30) REVERT: C 132 GLU cc_start: 0.9415 (mp0) cc_final: 0.9097 (mp0) REVERT: C 165 PHE cc_start: 0.8197 (p90) cc_final: 0.7938 (p90) REVERT: C 199 GLU cc_start: 0.9466 (tp30) cc_final: 0.9219 (tp30) REVERT: C 206 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8165 (ttpt) REVERT: C 208 LYS cc_start: 0.8658 (mtpp) cc_final: 0.8450 (mtpp) REVERT: C 216 ASP cc_start: 0.9074 (t70) cc_final: 0.8709 (t0) REVERT: C 250 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7711 (pp) REVERT: C 265 GLN cc_start: 0.9257 (mm110) cc_final: 0.8999 (mm-40) REVERT: C 297 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8725 (tm) REVERT: C 311 LYS cc_start: 0.8708 (tmtt) cc_final: 0.8244 (tmtt) REVERT: C 313 LEU cc_start: 0.9360 (mp) cc_final: 0.9076 (mp) REVERT: C 337 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7117 (tt) REVERT: C 348 TYR cc_start: 0.9115 (t80) cc_final: 0.8806 (t80) REVERT: C 352 GLU cc_start: 0.8660 (tp30) cc_final: 0.8390 (tp30) REVERT: C 386 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8233 (pmm) REVERT: C 407 ARG cc_start: 0.7584 (ttt180) cc_final: 0.6909 (ttt180) REVERT: C 420 MET cc_start: 0.7115 (mmm) cc_final: 0.6673 (mmm) REVERT: C 469 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.7831 (pt0) REVERT: C 470 ASP cc_start: 0.8639 (m-30) cc_final: 0.8327 (m-30) REVERT: C 490 PHE cc_start: 0.8370 (m-80) cc_final: 0.8092 (m-80) REVERT: C 510 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6778 (mm-30) REVERT: D 109 LYS cc_start: 0.8685 (mmtm) cc_final: 0.8356 (mptt) REVERT: D 161 ARG cc_start: 0.9523 (mpp-170) cc_final: 0.9068 (mtt90) REVERT: D 165 PHE cc_start: 0.7956 (p90) cc_final: 0.7721 (p90) REVERT: D 199 GLU cc_start: 0.9432 (tp30) cc_final: 0.9061 (tp30) REVERT: D 203 ARG cc_start: 0.9351 (ptp-110) cc_final: 0.9118 (ptp-110) REVERT: D 206 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8182 (ttpt) REVERT: D 216 ASP cc_start: 0.9053 (t70) cc_final: 0.8704 (t0) REVERT: D 261 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.8224 (p0) REVERT: D 265 GLN cc_start: 0.9251 (mm110) cc_final: 0.9001 (mm-40) REVERT: D 297 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8851 (tm) REVERT: D 311 LYS cc_start: 0.8699 (tmtt) cc_final: 0.7788 (tppt) REVERT: D 337 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7240 (tt) REVERT: D 386 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8191 (ppp) REVERT: D 400 TYR cc_start: 0.7711 (m-80) cc_final: 0.7295 (m-80) REVERT: D 407 ARG cc_start: 0.7317 (ttt180) cc_final: 0.6623 (ttt180) REVERT: D 420 MET cc_start: 0.7155 (mmm) cc_final: 0.6788 (mmm) REVERT: D 464 ILE cc_start: 0.8867 (pp) cc_final: 0.8628 (pp) REVERT: D 469 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.7564 (pt0) REVERT: D 470 ASP cc_start: 0.8706 (m-30) cc_final: 0.8346 (m-30) REVERT: D 488 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7565 (tp) REVERT: D 490 PHE cc_start: 0.8421 (m-80) cc_final: 0.7994 (m-80) REVERT: D 509 TYR cc_start: 0.7706 (p90) cc_final: 0.7433 (p90) REVERT: D 510 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6878 (mm-30) REVERT: E 32 TYR cc_start: 0.8574 (m-10) cc_final: 0.8360 (m-10) REVERT: E 62 LYS cc_start: 0.9128 (mmtp) cc_final: 0.8837 (mttm) REVERT: E 78 MET cc_start: 0.8167 (ttm) cc_final: 0.7722 (ttt) REVERT: E 109 LYS cc_start: 0.8855 (mmtm) cc_final: 0.8628 (mptt) REVERT: E 128 ARG cc_start: 0.9094 (mmm-85) cc_final: 0.8664 (mmt90) REVERT: E 132 GLU cc_start: 0.9492 (mp0) cc_final: 0.9135 (mp0) REVERT: E 165 PHE cc_start: 0.8121 (p90) cc_final: 0.7856 (p90) REVERT: E 166 LEU cc_start: 0.8211 (tp) cc_final: 0.7896 (tp) REVERT: E 185 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7596 (mt) REVERT: E 199 GLU cc_start: 0.9525 (tp30) cc_final: 0.9314 (tp30) REVERT: E 203 ARG cc_start: 0.9369 (ptp-110) cc_final: 0.9165 (ptp-110) REVERT: E 206 LYS cc_start: 0.8352 (tppt) cc_final: 0.7988 (tppt) REVERT: E 216 ASP cc_start: 0.9147 (t70) cc_final: 0.8780 (t0) REVERT: E 250 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7602 (pp) REVERT: E 297 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8706 (tm) REVERT: E 311 LYS cc_start: 0.8718 (tmtt) cc_final: 0.8289 (tmtt) REVERT: E 337 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7105 (tt) REVERT: E 386 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8399 (ppp) REVERT: E 400 TYR cc_start: 0.7805 (m-80) cc_final: 0.7074 (m-10) REVERT: E 407 ARG cc_start: 0.7453 (ttt180) cc_final: 0.6582 (ttt-90) REVERT: E 408 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8542 (mp) REVERT: E 420 MET cc_start: 0.7185 (mmm) cc_final: 0.6789 (mmm) REVERT: E 469 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7593 (pt0) REVERT: E 470 ASP cc_start: 0.8759 (m-30) cc_final: 0.8307 (m-30) REVERT: E 490 PHE cc_start: 0.8489 (m-80) cc_final: 0.8242 (m-80) REVERT: E 509 TYR cc_start: 0.8001 (p90) cc_final: 0.7778 (p90) REVERT: E 510 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6709 (mm-30) REVERT: F 32 TYR cc_start: 0.8494 (m-10) cc_final: 0.8256 (m-10) REVERT: F 62 LYS cc_start: 0.9275 (mmtp) cc_final: 0.9004 (mttm) REVERT: F 65 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9041 (pt) REVERT: F 78 MET cc_start: 0.8113 (ttm) cc_final: 0.7687 (ttt) REVERT: F 109 LYS cc_start: 0.8756 (mmtm) cc_final: 0.8427 (mptt) REVERT: F 132 GLU cc_start: 0.9471 (mp0) cc_final: 0.9137 (mp0) REVERT: F 165 PHE cc_start: 0.8342 (p90) cc_final: 0.7711 (p90) REVERT: F 166 LEU cc_start: 0.8135 (tp) cc_final: 0.7830 (tp) REVERT: F 199 GLU cc_start: 0.9485 (tp30) cc_final: 0.9209 (tp30) REVERT: F 206 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8123 (ttpt) REVERT: F 216 ASP cc_start: 0.9072 (t70) cc_final: 0.8717 (t0) REVERT: F 250 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7731 (pp) REVERT: F 261 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8383 (p0) REVERT: F 283 GLN cc_start: 0.8559 (tt0) cc_final: 0.8297 (mt0) REVERT: F 297 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8809 (tm) REVERT: F 311 LYS cc_start: 0.8688 (tmtt) cc_final: 0.8257 (tmtt) REVERT: F 337 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7185 (tt) REVERT: F 379 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9105 (tm) REVERT: F 386 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8160 (pmm) REVERT: F 407 ARG cc_start: 0.7657 (ttt180) cc_final: 0.7287 (ttt90) REVERT: F 408 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8566 (mp) REVERT: F 469 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.7562 (pt0) REVERT: F 470 ASP cc_start: 0.8682 (m-30) cc_final: 0.8266 (m-30) REVERT: F 490 PHE cc_start: 0.8478 (m-80) cc_final: 0.8258 (m-80) REVERT: F 509 TYR cc_start: 0.7950 (p90) cc_final: 0.7743 (p90) REVERT: F 510 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6444 (mm-30) REVERT: G 32 TYR cc_start: 0.8560 (m-80) cc_final: 0.8306 (m-10) REVERT: G 132 GLU cc_start: 0.9442 (mp0) cc_final: 0.9073 (mp0) REVERT: G 165 PHE cc_start: 0.8016 (p90) cc_final: 0.7696 (p90) REVERT: G 166 LEU cc_start: 0.8280 (tp) cc_final: 0.7972 (tp) REVERT: G 179 MET cc_start: 0.7021 (ttp) cc_final: 0.6808 (ptm) REVERT: G 199 GLU cc_start: 0.9473 (tp30) cc_final: 0.9123 (tp30) REVERT: G 206 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8130 (ttpt) REVERT: G 297 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8674 (tm) REVERT: G 311 LYS cc_start: 0.8689 (tmtt) cc_final: 0.8246 (tmtt) REVERT: G 337 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7129 (tt) REVERT: G 386 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8373 (pmm) REVERT: G 408 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8574 (mp) REVERT: G 420 MET cc_start: 0.6677 (mmm) cc_final: 0.6322 (mmm) REVERT: G 470 ASP cc_start: 0.8647 (m-30) cc_final: 0.8383 (m-30) REVERT: G 489 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8075 (tttt) REVERT: G 490 PHE cc_start: 0.8454 (m-80) cc_final: 0.8087 (m-80) REVERT: G 509 TYR cc_start: 0.7998 (p90) cc_final: 0.7789 (p90) REVERT: H 62 LYS cc_start: 0.9322 (mmtp) cc_final: 0.9024 (mttm) REVERT: H 78 MET cc_start: 0.7643 (ttt) cc_final: 0.7283 (ttt) REVERT: H 109 LYS cc_start: 0.8727 (mmtm) cc_final: 0.8516 (mptt) REVERT: H 161 ARG cc_start: 0.9568 (mpp-170) cc_final: 0.8960 (mtm-85) REVERT: H 165 PHE cc_start: 0.8025 (p90) cc_final: 0.7768 (p90) REVERT: H 186 VAL cc_start: 0.9355 (m) cc_final: 0.8913 (m) REVERT: H 199 GLU cc_start: 0.9485 (tp30) cc_final: 0.8839 (tp30) REVERT: H 203 ARG cc_start: 0.9359 (ptp-110) cc_final: 0.9030 (ptp-110) REVERT: H 206 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8024 (ttpt) REVERT: H 216 ASP cc_start: 0.8995 (t70) cc_final: 0.8641 (t0) REVERT: H 250 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7767 (pp) REVERT: H 297 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8832 (tm) REVERT: H 311 LYS cc_start: 0.8689 (tmtt) cc_final: 0.8246 (tmtt) REVERT: H 337 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7198 (tt) REVERT: H 348 TYR cc_start: 0.8873 (t80) cc_final: 0.8631 (t80) REVERT: H 386 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8088 (pmm) REVERT: H 469 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.7662 (pt0) REVERT: H 470 ASP cc_start: 0.8778 (m-30) cc_final: 0.8391 (m-30) REVERT: H 482 MET cc_start: 0.8773 (tpt) cc_final: 0.8469 (tpt) REVERT: H 487 GLU cc_start: 0.8373 (pm20) cc_final: 0.7989 (pm20) REVERT: H 490 PHE cc_start: 0.8474 (m-80) cc_final: 0.8065 (m-80) outliers start: 266 outliers final: 167 residues processed: 1145 average time/residue: 0.1872 time to fit residues: 348.5862 Evaluate side-chains 1197 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 972 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 186 VAL 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 261 ASP Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 510 GLU 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 120 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 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 386 MET Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 186 VAL 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 273 LEU Chi-restraints excluded: chain F residue 294 TYR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 353 TYR Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 222 ILE Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 294 TYR 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 379 LEU Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 469 GLN Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 494 THR Chi-restraints excluded: chain H residue 499 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 221 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 310 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 316 optimal weight: 0.8980 chunk 311 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS B 283 GLN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS D 283 GLN ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN E 465 GLN ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 469 GLN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN ** G 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 GLN ** G 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 253 HIS H 283 GLN H 303 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.163899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.127172 restraints weight = 52100.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.132612 restraints weight = 30227.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.136449 restraints weight = 20719.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.139204 restraints weight = 15642.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.141096 restraints weight = 12592.289| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 31592 Z= 0.179 Angle : 0.882 11.313 42888 Z= 0.416 Chirality : 0.050 0.223 4888 Planarity : 0.005 0.082 5328 Dihedral : 12.937 139.210 4673 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 8.71 % Allowed : 31.17 % Favored : 60.12 % 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: -2.18 (0.13), residues: 3880 helix: -1.39 (0.14), residues: 1216 sheet: -2.44 (0.20), residues: 528 loop : -1.12 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 322 TYR 0.032 0.002 TYR H 509 PHE 0.020 0.001 PHE F 90 HIS 0.008 0.001 HIS H 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (31576) covalent geometry : angle 0.88208 / 0.42 (42888) hydrogen bonds : bond 0.03540 / 2.31 ( 832) hydrogen bonds : angle 5.31378 / 3.67 ( 2376) Misc. bond : bond 0.00042 / 0.03 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1289 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 278 poor density : 1011 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8635 (m-10) cc_final: 0.8391 (m-10) REVERT: A 51 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8060 (pp) REVERT: A 109 LYS cc_start: 0.8887 (mmtm) cc_final: 0.8670 (mppt) REVERT: A 128 ARG cc_start: 0.8556 (mmt90) cc_final: 0.8221 (mmt180) REVERT: A 186 VAL cc_start: 0.9332 (m) cc_final: 0.9099 (m) REVERT: A 199 GLU cc_start: 0.9460 (tp30) cc_final: 0.9092 (tp30) REVERT: A 202 GLN cc_start: 0.9444 (mt0) cc_final: 0.8625 (pp30) REVERT: A 206 LYS cc_start: 0.8355 (mtmt) cc_final: 0.7689 (ttpt) REVERT: A 216 ASP cc_start: 0.9024 (t70) cc_final: 0.8723 (t0) REVERT: A 250 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7844 (pp) REVERT: A 285 ASN cc_start: 0.9499 (m110) cc_final: 0.9173 (m110) REVERT: A 297 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8752 (tm) REVERT: A 311 LYS cc_start: 0.8711 (tmtt) cc_final: 0.8271 (tmtt) REVERT: A 337 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7155 (tt) REVERT: A 352 GLU cc_start: 0.8855 (tp30) cc_final: 0.8506 (tp30) REVERT: A 385 MET cc_start: 0.7703 (ttt) cc_final: 0.7356 (ttt) REVERT: A 386 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8121 (ppp) REVERT: A 420 MET cc_start: 0.6833 (mmm) cc_final: 0.6453 (mmm) REVERT: A 469 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.7581 (pt0) REVERT: A 470 ASP cc_start: 0.8636 (m-30) cc_final: 0.8337 (m-30) REVERT: A 490 PHE cc_start: 0.8471 (m-80) cc_final: 0.8140 (m-80) REVERT: A 510 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6708 (mm-30) REVERT: B 32 TYR cc_start: 0.8596 (m-10) cc_final: 0.8381 (m-10) REVERT: B 109 LYS cc_start: 0.8727 (mmtm) cc_final: 0.8507 (mptt) REVERT: B 165 PHE cc_start: 0.8022 (p90) cc_final: 0.7736 (p90) REVERT: B 199 GLU cc_start: 0.9447 (tp30) cc_final: 0.8882 (tp30) REVERT: B 202 GLN cc_start: 0.9400 (mm-40) cc_final: 0.8436 (pp30) REVERT: B 206 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8108 (ttpt) REVERT: B 216 ASP cc_start: 0.8972 (t70) cc_final: 0.8616 (t0) REVERT: B 258 TYR cc_start: 0.7898 (t80) cc_final: 0.7652 (t80) REVERT: B 265 GLN cc_start: 0.9264 (mm110) cc_final: 0.8992 (mm-40) REVERT: B 311 LYS cc_start: 0.8758 (tmtt) cc_final: 0.8316 (tmtt) REVERT: B 337 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7261 (tt) REVERT: B 386 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8290 (pmm) REVERT: B 420 MET cc_start: 0.7399 (mmm) cc_final: 0.7033 (mmm) REVERT: B 469 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7423 (pt0) REVERT: B 470 ASP cc_start: 0.8757 (m-30) cc_final: 0.8317 (m-30) REVERT: B 490 PHE cc_start: 0.8559 (m-80) cc_final: 0.8253 (m-80) REVERT: C 32 TYR cc_start: 0.8668 (m-10) cc_final: 0.8421 (m-10) REVERT: C 78 MET cc_start: 0.7383 (ttt) cc_final: 0.6996 (tmm) REVERT: C 128 ARG cc_start: 0.9025 (mmm-85) cc_final: 0.8581 (mmt90) REVERT: C 132 GLU cc_start: 0.9424 (mp0) cc_final: 0.9100 (mp0) REVERT: C 165 PHE cc_start: 0.8268 (p90) cc_final: 0.7972 (p90) REVERT: C 179 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7369 (pmm) REVERT: C 199 GLU cc_start: 0.9477 (tp30) cc_final: 0.9222 (tp30) REVERT: C 202 GLN cc_start: 0.9374 (mm-40) cc_final: 0.8564 (mm-40) REVERT: C 206 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8129 (ttpt) REVERT: C 208 LYS cc_start: 0.8666 (mtpp) cc_final: 0.8427 (ttmm) REVERT: C 214 GLU cc_start: 0.9280 (mm-30) cc_final: 0.9019 (mp0) REVERT: C 216 ASP cc_start: 0.9102 (t70) cc_final: 0.8756 (t0) REVERT: C 250 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7920 (pp) REVERT: C 297 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8788 (tm) REVERT: C 311 LYS cc_start: 0.8697 (tmtt) cc_final: 0.8244 (tmtt) REVERT: C 337 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7083 (tt) REVERT: C 348 TYR cc_start: 0.9120 (t80) cc_final: 0.8787 (t80) REVERT: C 352 GLU cc_start: 0.8725 (tp30) cc_final: 0.8415 (tp30) REVERT: C 386 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8477 (pmm) REVERT: C 400 TYR cc_start: 0.7812 (m-80) cc_final: 0.7488 (m-10) REVERT: C 408 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8568 (mp) REVERT: C 420 MET cc_start: 0.7312 (mmm) cc_final: 0.6847 (mmm) REVERT: C 470 ASP cc_start: 0.8662 (m-30) cc_final: 0.8318 (m-30) REVERT: C 490 PHE cc_start: 0.8473 (m-80) cc_final: 0.8139 (m-80) REVERT: C 509 TYR cc_start: 0.7347 (p90) cc_final: 0.6918 (p90) REVERT: C 512 ARG cc_start: 0.7407 (ttp-110) cc_final: 0.7180 (ttp-170) REVERT: D 32 TYR cc_start: 0.8626 (m-10) cc_final: 0.8345 (m-10) REVERT: D 109 LYS cc_start: 0.8681 (mmtm) cc_final: 0.8401 (mptt) REVERT: D 128 ARG cc_start: 0.8766 (mmt90) cc_final: 0.8419 (mmt90) REVERT: D 165 PHE cc_start: 0.7985 (p90) cc_final: 0.7686 (p90) REVERT: D 179 MET cc_start: 0.7816 (mtm) cc_final: 0.7381 (pmm) REVERT: D 199 GLU cc_start: 0.9464 (tp30) cc_final: 0.9116 (tp30) REVERT: D 203 ARG cc_start: 0.9348 (ptp-110) cc_final: 0.9140 (ptp-110) REVERT: D 206 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8154 (ttpt) REVERT: D 216 ASP cc_start: 0.9055 (t70) cc_final: 0.8704 (t0) REVERT: D 261 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8362 (p0) REVERT: D 265 GLN cc_start: 0.9237 (mm110) cc_final: 0.9028 (mm-40) REVERT: D 309 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8764 (pt0) REVERT: D 311 LYS cc_start: 0.8694 (tmtt) cc_final: 0.7709 (tppt) REVERT: D 337 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7248 (tt) REVERT: D 385 MET cc_start: 0.8105 (ttp) cc_final: 0.7807 (ttt) REVERT: D 386 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8217 (pmm) REVERT: D 400 TYR cc_start: 0.7721 (m-80) cc_final: 0.7294 (m-80) REVERT: D 407 ARG cc_start: 0.7296 (ttt180) cc_final: 0.6595 (ttt180) REVERT: D 420 MET cc_start: 0.7354 (mmm) cc_final: 0.6971 (mmm) REVERT: D 469 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.7540 (pt0) REVERT: D 470 ASP cc_start: 0.8759 (m-30) cc_final: 0.8354 (m-30) REVERT: D 488 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7438 (tp) REVERT: D 490 PHE cc_start: 0.8445 (m-80) cc_final: 0.7904 (m-80) REVERT: D 510 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6924 (mm-30) REVERT: E 32 TYR cc_start: 0.8612 (m-10) cc_final: 0.8394 (m-10) REVERT: E 78 MET cc_start: 0.8251 (ttm) cc_final: 0.7820 (ttt) REVERT: E 128 ARG cc_start: 0.9084 (mmm-85) cc_final: 0.8552 (mmt90) REVERT: E 132 GLU cc_start: 0.9492 (mp0) cc_final: 0.9113 (mp0) REVERT: E 165 PHE cc_start: 0.8135 (p90) cc_final: 0.7528 (p90) REVERT: E 166 LEU cc_start: 0.8175 (tp) cc_final: 0.7837 (tp) REVERT: E 185 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7492 (mt) REVERT: E 199 GLU cc_start: 0.9540 (tp30) cc_final: 0.9320 (tp30) REVERT: E 203 ARG cc_start: 0.9352 (ptp-110) cc_final: 0.9136 (ptp-110) REVERT: E 206 LYS cc_start: 0.8458 (tppt) cc_final: 0.8022 (tppt) REVERT: E 216 ASP cc_start: 0.9150 (t70) cc_final: 0.8788 (t0) REVERT: E 250 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7776 (pp) REVERT: E 265 GLN cc_start: 0.9291 (mm110) cc_final: 0.9061 (mm-40) REVERT: E 297 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8796 (tm) REVERT: E 311 LYS cc_start: 0.8672 (tmtt) cc_final: 0.8227 (tmtt) REVERT: E 337 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7078 (tt) REVERT: E 386 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8454 (pmm) REVERT: E 400 TYR cc_start: 0.7812 (m-80) cc_final: 0.7596 (m-80) REVERT: E 408 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8562 (mp) REVERT: E 420 MET cc_start: 0.7354 (mmm) cc_final: 0.6928 (mmm) REVERT: E 469 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.7739 (pt0) REVERT: E 470 ASP cc_start: 0.8790 (m-30) cc_final: 0.8387 (m-30) REVERT: E 488 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7685 (tp) REVERT: E 490 PHE cc_start: 0.8540 (m-80) cc_final: 0.8266 (m-80) REVERT: E 510 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6631 (mm-30) REVERT: F 62 LYS cc_start: 0.9339 (mmtp) cc_final: 0.9042 (mttm) REVERT: F 65 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9096 (pt) REVERT: F 78 MET cc_start: 0.8092 (ttm) cc_final: 0.7704 (ttt) REVERT: F 109 LYS cc_start: 0.8718 (mmtm) cc_final: 0.8433 (mptt) REVERT: F 132 GLU cc_start: 0.9464 (mp0) cc_final: 0.9143 (mp0) REVERT: F 165 PHE cc_start: 0.8353 (p90) cc_final: 0.7752 (p90) REVERT: F 166 LEU cc_start: 0.8121 (tp) cc_final: 0.7809 (tp) REVERT: F 199 GLU cc_start: 0.9497 (tp30) cc_final: 0.9134 (tp30) REVERT: F 203 ARG cc_start: 0.9312 (ptp-110) cc_final: 0.9033 (ptp-110) REVERT: F 206 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8072 (ttpt) REVERT: F 216 ASP cc_start: 0.9084 (t70) cc_final: 0.8728 (t0) REVERT: F 224 ARG cc_start: 0.8836 (ttm170) cc_final: 0.8601 (ttm170) REVERT: F 261 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8308 (p0) REVERT: F 283 GLN cc_start: 0.8710 (tt0) cc_final: 0.8450 (mt0) REVERT: F 311 LYS cc_start: 0.8721 (tmtt) cc_final: 0.8278 (tmtt) REVERT: F 337 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7181 (tt) REVERT: F 379 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9142 (tm) REVERT: F 386 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8313 (pmm) REVERT: F 469 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.7680 (pt0) REVERT: F 470 ASP cc_start: 0.8706 (m-30) cc_final: 0.8250 (m-30) REVERT: F 490 PHE cc_start: 0.8561 (m-80) cc_final: 0.8277 (m-80) REVERT: F 510 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6545 (mm-30) REVERT: G 32 TYR cc_start: 0.8557 (m-80) cc_final: 0.8329 (m-10) REVERT: G 74 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.7529 (p) REVERT: G 128 ARG cc_start: 0.8789 (mmt90) cc_final: 0.8386 (mmt90) REVERT: G 165 PHE cc_start: 0.8073 (p90) cc_final: 0.7744 (p90) REVERT: G 166 LEU cc_start: 0.8161 (tp) cc_final: 0.7827 (tp) REVERT: G 199 GLU cc_start: 0.9491 (tp30) cc_final: 0.9136 (tp30) REVERT: G 206 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8124 (ttpt) REVERT: G 208 LYS cc_start: 0.8045 (ttmm) cc_final: 0.7606 (mtmm) REVERT: G 216 ASP cc_start: 0.9136 (t70) cc_final: 0.8840 (t0) REVERT: G 261 ASP cc_start: 0.8981 (t0) cc_final: 0.8633 (m-30) REVERT: G 297 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8695 (tm) REVERT: G 311 LYS cc_start: 0.8677 (tmtt) cc_final: 0.8231 (tmtt) REVERT: G 337 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7107 (tt) REVERT: G 352 GLU cc_start: 0.8814 (tp30) cc_final: 0.8493 (tp30) REVERT: G 386 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8413 (pmm) REVERT: G 407 ARG cc_start: 0.7486 (ttt180) cc_final: 0.7218 (tpt-90) REVERT: G 408 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8473 (mp) REVERT: G 420 MET cc_start: 0.7010 (mmm) cc_final: 0.6576 (mmm) REVERT: G 465 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7576 (mt0) REVERT: G 469 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.7679 (pt0) REVERT: G 470 ASP cc_start: 0.8678 (m-30) cc_final: 0.8377 (m-30) REVERT: G 488 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7760 (tp) REVERT: G 489 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7951 (tttt) REVERT: G 490 PHE cc_start: 0.8489 (m-80) cc_final: 0.8185 (m-80) REVERT: H 62 LYS cc_start: 0.9332 (mmtp) cc_final: 0.9040 (mttm) REVERT: H 66 VAL cc_start: 0.8884 (OUTLIER) cc_final: 0.8538 (p) REVERT: H 78 MET cc_start: 0.7668 (ttt) cc_final: 0.7287 (ttt) REVERT: H 109 LYS cc_start: 0.8742 (mmtm) cc_final: 0.8535 (mptt) REVERT: H 128 ARG cc_start: 0.8919 (mmm-85) cc_final: 0.8679 (mmt90) REVERT: H 165 PHE cc_start: 0.8037 (p90) cc_final: 0.7411 (p90) REVERT: H 179 MET cc_start: 0.7291 (ptm) cc_final: 0.7087 (ptm) REVERT: H 186 VAL cc_start: 0.9373 (m) cc_final: 0.8937 (m) REVERT: H 199 GLU cc_start: 0.9486 (tp30) cc_final: 0.9153 (tp30) REVERT: H 203 ARG cc_start: 0.9352 (ptp-110) cc_final: 0.9136 (ptp-110) REVERT: H 206 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.7967 (ttpt) REVERT: H 216 ASP cc_start: 0.9017 (t70) cc_final: 0.8694 (t0) REVERT: H 250 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7811 (pp) REVERT: H 262 LEU cc_start: 0.9151 (tp) cc_final: 0.8914 (tp) REVERT: H 297 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8831 (tm) REVERT: H 311 LYS cc_start: 0.8679 (tmtt) cc_final: 0.8252 (tmtt) REVERT: H 337 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7202 (tt) REVERT: H 386 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8238 (pmm) REVERT: H 469 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.7668 (pt0) REVERT: H 470 ASP cc_start: 0.8784 (m-30) cc_final: 0.8397 (m-30) REVERT: H 488 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8075 (tp) REVERT: H 490 PHE cc_start: 0.8518 (m-80) cc_final: 0.8101 (m-80) REVERT: H 509 TYR cc_start: 0.7622 (p90) cc_final: 0.7319 (p90) outliers start: 278 outliers final: 185 residues processed: 1135 average time/residue: 0.1825 time to fit residues: 336.8476 Evaluate side-chains 1236 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 245 poor density : 991 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 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 120 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 386 MET 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 499 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 235 LEU 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 297 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 499 VAL 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 120 VAL Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 510 GLU 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 120 VAL Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 353 TYR Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 186 VAL 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 244 LEU 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 297 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 353 TYR Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 465 GLN Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 222 ILE Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 294 TYR 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 379 LEU Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 469 GLN Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 494 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 203 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 255 optimal weight: 3.9990 chunk 277 optimal weight: 4.9990 chunk 243 optimal weight: 0.7980 chunk 347 optimal weight: 9.9990 chunk 307 optimal weight: 5.9990 chunk 226 optimal weight: 2.9990 chunk 278 optimal weight: 9.9990 chunk 311 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN D 469 GLN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 HIS ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN G 465 GLN ** G 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 GLN H 303 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 469 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.166876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.128053 restraints weight = 52019.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.133777 restraints weight = 30115.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.137823 restraints weight = 20645.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.140717 restraints weight = 15577.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.142813 restraints weight = 12569.521| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 31592 Z= 0.210 Angle : 0.914 12.860 42888 Z= 0.437 Chirality : 0.051 0.240 4888 Planarity : 0.005 0.095 5328 Dihedral : 12.798 138.769 4669 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 8.65 % Allowed : 31.58 % Favored : 59.77 % 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: -2.23 (0.13), residues: 3880 helix: -1.45 (0.13), residues: 1232 sheet: -2.52 (0.20), residues: 528 loop : -1.12 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 355 TYR 0.031 0.002 TYR G 509 PHE 0.017 0.002 PHE D 90 HIS 0.015 0.001 HIS G 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (31576) covalent geometry : angle 0.91380 / 0.44 (42888) hydrogen bonds : bond 0.03742 / 2.46 ( 832) hydrogen bonds : angle 5.43192 / 3.74 ( 2376) Misc. bond : bond 0.00048 / 0.03 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1278 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 276 poor density : 1002 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8598 (m-10) cc_final: 0.8353 (m-10) REVERT: A 51 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8062 (pp) REVERT: A 109 LYS cc_start: 0.8866 (mmtm) cc_final: 0.8658 (mptt) REVERT: A 128 ARG cc_start: 0.8518 (mmt90) cc_final: 0.8188 (mmt180) REVERT: A 216 ASP cc_start: 0.9049 (t70) cc_final: 0.8743 (t0) REVERT: A 250 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8029 (pp) REVERT: A 261 ASP cc_start: 0.9029 (t0) cc_final: 0.8725 (m-30) REVERT: A 311 LYS cc_start: 0.8662 (tmtt) cc_final: 0.8214 (tmtt) REVERT: A 337 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7195 (tt) REVERT: A 352 GLU cc_start: 0.8904 (tp30) cc_final: 0.8656 (tp30) REVERT: A 385 MET cc_start: 0.7815 (ttt) cc_final: 0.7446 (ttt) REVERT: A 386 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8186 (ppp) REVERT: A 420 MET cc_start: 0.7325 (mmm) cc_final: 0.6861 (mmm) REVERT: A 469 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.7949 (pt0) REVERT: A 470 ASP cc_start: 0.8644 (m-30) cc_final: 0.8409 (m-30) REVERT: A 490 PHE cc_start: 0.8484 (m-80) cc_final: 0.8149 (m-80) REVERT: B 109 LYS cc_start: 0.8737 (mmtm) cc_final: 0.8534 (mptt) REVERT: B 128 ARG cc_start: 0.9004 (mmm-85) cc_final: 0.8618 (mmt90) REVERT: B 165 PHE cc_start: 0.7981 (p90) cc_final: 0.7595 (p90) REVERT: B 202 GLN cc_start: 0.9421 (mm-40) cc_final: 0.9111 (mm-40) REVERT: B 216 ASP cc_start: 0.8971 (t70) cc_final: 0.8601 (t0) REVERT: B 250 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7806 (pp) REVERT: B 265 GLN cc_start: 0.9277 (mm110) cc_final: 0.8984 (mm-40) REVERT: B 297 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8933 (tm) REVERT: B 311 LYS cc_start: 0.8741 (tmtt) cc_final: 0.8274 (tmtt) REVERT: B 337 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7306 (tt) REVERT: B 386 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8336 (pmm) REVERT: B 420 MET cc_start: 0.7293 (mmm) cc_final: 0.6918 (mmm) REVERT: B 469 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.7757 (pt0) REVERT: B 488 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7651 (tp) REVERT: B 490 PHE cc_start: 0.8515 (m-80) cc_final: 0.8170 (m-80) REVERT: C 32 TYR cc_start: 0.8659 (m-10) cc_final: 0.8351 (m-10) REVERT: C 78 MET cc_start: 0.7459 (ttt) cc_final: 0.7084 (tmm) REVERT: C 128 ARG cc_start: 0.9015 (mmm-85) cc_final: 0.8659 (mmt90) REVERT: C 165 PHE cc_start: 0.8336 (p90) cc_final: 0.8035 (p90) REVERT: C 199 GLU cc_start: 0.9513 (tp30) cc_final: 0.9261 (tp30) REVERT: C 202 GLN cc_start: 0.9393 (mm-40) cc_final: 0.8613 (mm-40) REVERT: C 206 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8115 (ttpt) REVERT: C 208 LYS cc_start: 0.8649 (mtpp) cc_final: 0.8273 (mtmm) REVERT: C 214 GLU cc_start: 0.9301 (mm-30) cc_final: 0.9036 (mp0) REVERT: C 216 ASP cc_start: 0.9122 (t70) cc_final: 0.8772 (t0) REVERT: C 250 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8007 (pp) REVERT: C 297 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8878 (tm) REVERT: C 311 LYS cc_start: 0.8625 (tmtt) cc_final: 0.8247 (ttpp) REVERT: C 337 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7249 (tt) REVERT: C 348 TYR cc_start: 0.9153 (t80) cc_final: 0.8806 (t80) REVERT: C 352 GLU cc_start: 0.8766 (tp30) cc_final: 0.8444 (tp30) REVERT: C 386 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8637 (pmm) REVERT: C 400 TYR cc_start: 0.7746 (m-80) cc_final: 0.7489 (m-10) REVERT: C 420 MET cc_start: 0.7349 (mmm) cc_final: 0.6807 (mmm) REVERT: C 470 ASP cc_start: 0.8669 (m-30) cc_final: 0.8378 (m-30) REVERT: C 482 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8654 (ttp) REVERT: C 490 PHE cc_start: 0.8552 (m-80) cc_final: 0.8106 (m-80) REVERT: C 512 ARG cc_start: 0.7535 (ttp-110) cc_final: 0.7216 (ttp-170) REVERT: D 32 TYR cc_start: 0.8682 (m-10) cc_final: 0.8431 (m-10) REVERT: D 73 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.7392 (t) REVERT: D 109 LYS cc_start: 0.8654 (mmtm) cc_final: 0.8406 (mptt) REVERT: D 128 ARG cc_start: 0.8789 (mmt90) cc_final: 0.8356 (mmt90) REVERT: D 165 PHE cc_start: 0.7980 (p90) cc_final: 0.7628 (p90) REVERT: D 179 MET cc_start: 0.7923 (mtm) cc_final: 0.7435 (pmm) REVERT: D 199 GLU cc_start: 0.9496 (tp30) cc_final: 0.9100 (tp30) REVERT: D 202 GLN cc_start: 0.9379 (mm-40) cc_final: 0.8956 (mm-40) REVERT: D 203 ARG cc_start: 0.9354 (ptp-110) cc_final: 0.9110 (ptp-110) REVERT: D 216 ASP cc_start: 0.9100 (t70) cc_final: 0.8719 (t0) REVERT: D 261 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8326 (p0) REVERT: D 309 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8861 (pt0) REVERT: D 311 LYS cc_start: 0.8681 (tmtt) cc_final: 0.7696 (tppt) REVERT: D 337 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7282 (tt) REVERT: D 385 MET cc_start: 0.8075 (ttp) cc_final: 0.7842 (ttt) REVERT: D 386 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8048 (ppp) REVERT: D 400 TYR cc_start: 0.7712 (m-80) cc_final: 0.7309 (m-80) REVERT: D 407 ARG cc_start: 0.7291 (ttt180) cc_final: 0.6622 (ttt180) REVERT: D 420 MET cc_start: 0.7235 (mmm) cc_final: 0.6862 (mmm) REVERT: D 469 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.7726 (pt0) REVERT: D 470 ASP cc_start: 0.8750 (m-30) cc_final: 0.8423 (m-30) REVERT: D 488 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7042 (tt) REVERT: D 490 PHE cc_start: 0.8470 (m-80) cc_final: 0.7804 (m-80) REVERT: D 510 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6815 (mm-30) REVERT: E 32 TYR cc_start: 0.8604 (m-10) cc_final: 0.8351 (m-10) REVERT: E 128 ARG cc_start: 0.9109 (mmm-85) cc_final: 0.8705 (mmm-85) REVERT: E 165 PHE cc_start: 0.8230 (p90) cc_final: 0.7909 (p90) REVERT: E 166 LEU cc_start: 0.8199 (tp) cc_final: 0.7875 (tp) REVERT: E 179 MET cc_start: 0.7391 (pmm) cc_final: 0.6810 (pmm) REVERT: E 185 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7463 (mt) REVERT: E 206 LYS cc_start: 0.8520 (tppt) cc_final: 0.8095 (tppt) REVERT: E 214 GLU cc_start: 0.9323 (mm-30) cc_final: 0.9078 (mp0) REVERT: E 216 ASP cc_start: 0.9178 (t70) cc_final: 0.8815 (t0) REVERT: E 250 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.7947 (pp) REVERT: E 265 GLN cc_start: 0.9306 (mm110) cc_final: 0.9094 (mm-40) REVERT: E 297 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8878 (tm) REVERT: E 311 LYS cc_start: 0.8720 (tmtt) cc_final: 0.8286 (tmtt) REVERT: E 337 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7066 (tt) REVERT: E 386 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8131 (ppp) REVERT: E 408 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8401 (mp) REVERT: E 420 MET cc_start: 0.7361 (mmm) cc_final: 0.6822 (mmm) REVERT: E 466 HIS cc_start: 0.8518 (OUTLIER) cc_final: 0.7757 (t-90) REVERT: E 469 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.7705 (pt0) REVERT: E 470 ASP cc_start: 0.8829 (m-30) cc_final: 0.8384 (m-30) REVERT: E 488 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7624 (tp) REVERT: E 490 PHE cc_start: 0.8478 (m-80) cc_final: 0.8158 (m-80) REVERT: E 509 TYR cc_start: 0.7521 (p90) cc_final: 0.7200 (p90) REVERT: F 32 TYR cc_start: 0.8666 (m-10) cc_final: 0.8390 (m-10) REVERT: F 62 LYS cc_start: 0.9263 (mmtp) cc_final: 0.8985 (mttm) REVERT: F 66 VAL cc_start: 0.8606 (OUTLIER) cc_final: 0.8153 (p) REVERT: F 78 MET cc_start: 0.8190 (ttm) cc_final: 0.7578 (ttp) REVERT: F 109 LYS cc_start: 0.8702 (mmtm) cc_final: 0.8412 (mptt) REVERT: F 132 GLU cc_start: 0.9474 (mp0) cc_final: 0.9158 (mp0) REVERT: F 165 PHE cc_start: 0.8364 (p90) cc_final: 0.7996 (p90) REVERT: F 166 LEU cc_start: 0.8204 (tp) cc_final: 0.7878 (tp) REVERT: F 199 GLU cc_start: 0.9513 (tp30) cc_final: 0.9155 (tp30) REVERT: F 203 ARG cc_start: 0.9314 (ptp-110) cc_final: 0.9018 (ptp-110) REVERT: F 206 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8073 (ttpt) REVERT: F 216 ASP cc_start: 0.9118 (t70) cc_final: 0.8742 (t0) REVERT: F 224 ARG cc_start: 0.8925 (ttm170) cc_final: 0.8602 (ttm170) REVERT: F 250 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.7876 (pp) REVERT: F 261 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8403 (p0) REVERT: F 283 GLN cc_start: 0.8823 (tt0) cc_final: 0.8608 (mt0) REVERT: F 297 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8871 (tm) REVERT: F 311 LYS cc_start: 0.8713 (tmtt) cc_final: 0.8258 (tmtt) REVERT: F 337 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7261 (tt) REVERT: F 379 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9192 (tm) REVERT: F 386 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8410 (pmm) REVERT: F 469 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.7763 (pt0) REVERT: F 470 ASP cc_start: 0.8678 (m-30) cc_final: 0.8304 (m-30) REVERT: F 490 PHE cc_start: 0.8555 (m-80) cc_final: 0.8195 (m-80) REVERT: F 509 TYR cc_start: 0.7412 (p90) cc_final: 0.6877 (p90) REVERT: F 510 GLU cc_start: 0.7043 (mm-30) cc_final: 0.6490 (mm-30) REVERT: F 514 PHE cc_start: 0.7758 (p90) cc_final: 0.7047 (p90) REVERT: G 32 TYR cc_start: 0.8567 (m-10) cc_final: 0.8329 (m-10) REVERT: G 128 ARG cc_start: 0.8799 (mmt90) cc_final: 0.8471 (mmt90) REVERT: G 129 ASP cc_start: 0.9078 (m-30) cc_final: 0.8867 (m-30) REVERT: G 132 GLU cc_start: 0.9446 (mp0) cc_final: 0.9154 (mp0) REVERT: G 165 PHE cc_start: 0.8159 (p90) cc_final: 0.7648 (p90) REVERT: G 166 LEU cc_start: 0.8189 (tp) cc_final: 0.7876 (tp) REVERT: G 199 GLU cc_start: 0.9512 (tp30) cc_final: 0.9166 (tp30) REVERT: G 206 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8144 (ttpt) REVERT: G 216 ASP cc_start: 0.9154 (t70) cc_final: 0.8851 (t0) REVERT: G 297 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8785 (tm) REVERT: G 311 LYS cc_start: 0.8665 (tmtt) cc_final: 0.8235 (tmtt) REVERT: G 337 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7121 (tt) REVERT: G 352 GLU cc_start: 0.8826 (tp30) cc_final: 0.8524 (tp30) REVERT: G 386 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8473 (pmm) REVERT: G 407 ARG cc_start: 0.7501 (ttt180) cc_final: 0.7263 (ttt180) REVERT: G 408 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8614 (mp) REVERT: G 420 MET cc_start: 0.7135 (mmm) cc_final: 0.6709 (mmm) REVERT: G 470 ASP cc_start: 0.8694 (m-30) cc_final: 0.8390 (m-30) REVERT: G 488 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7832 (tp) REVERT: G 489 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.8007 (ttmt) REVERT: G 490 PHE cc_start: 0.8461 (m-80) cc_final: 0.8104 (m-80) REVERT: H 62 LYS cc_start: 0.9307 (mmtp) cc_final: 0.8999 (mttm) REVERT: H 66 VAL cc_start: 0.8840 (OUTLIER) cc_final: 0.8466 (p) REVERT: H 109 LYS cc_start: 0.8723 (mmtm) cc_final: 0.8511 (mptt) REVERT: H 128 ARG cc_start: 0.8997 (mmm-85) cc_final: 0.8547 (mmt90) REVERT: H 165 PHE cc_start: 0.8044 (p90) cc_final: 0.7446 (p90) REVERT: H 199 GLU cc_start: 0.9507 (tp30) cc_final: 0.9137 (tp30) REVERT: H 203 ARG cc_start: 0.9323 (ptp-110) cc_final: 0.9079 (ptp-110) REVERT: H 206 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8001 (ttpt) REVERT: H 216 ASP cc_start: 0.9037 (t70) cc_final: 0.8704 (t0) REVERT: H 250 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7890 (pp) REVERT: H 297 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8871 (tm) REVERT: H 311 LYS cc_start: 0.8724 (tmtt) cc_final: 0.8285 (tmtt) REVERT: H 337 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7157 (tt) REVERT: H 386 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8351 (pmm) REVERT: H 469 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.7696 (pt0) REVERT: H 470 ASP cc_start: 0.8732 (m-30) cc_final: 0.8359 (m-30) REVERT: H 488 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8156 (tp) REVERT: H 490 PHE cc_start: 0.8524 (m-80) cc_final: 0.8096 (m-80) REVERT: H 509 TYR cc_start: 0.7579 (p90) cc_final: 0.7324 (p90) outliers start: 276 outliers final: 193 residues processed: 1124 average time/residue: 0.1799 time to fit residues: 330.2015 Evaluate side-chains 1223 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 251 poor density : 972 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 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 120 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 331 CYS 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 353 TYR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 386 MET 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 B residue 42 ILE Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 235 LEU 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 297 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 488 LEU 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 120 VAL Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 244 LEU 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 306 THR Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 482 MET Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 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 309 GLN Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 353 TYR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 120 VAL 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 244 LEU Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 353 TYR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 466 HIS 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 61 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 353 TYR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 222 ILE Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 294 TYR 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 370 VAL 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 389 LEU Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 469 GLN Chi-restraints excluded: chain H residue 485 SER Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 494 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 353 optimal weight: 7.9990 chunk 240 optimal weight: 10.0000 chunk 300 optimal weight: 0.9990 chunk 176 optimal weight: 0.5980 chunk 383 optimal weight: 0.9990 chunk 59 optimal weight: 0.0870 chunk 351 optimal weight: 5.9990 chunk 206 optimal weight: 10.0000 chunk 197 optimal weight: 0.0770 chunk 261 optimal weight: 9.9990 chunk 164 optimal weight: 0.2980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN A 312 ASN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 GLN C 465 GLN D 198 ASN D 283 GLN ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 298 GLN G 465 GLN G 469 GLN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.171223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.135114 restraints weight = 51676.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.140896 restraints weight = 29763.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.144884 restraints weight = 20105.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.147654 restraints weight = 14988.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.149738 restraints weight = 11951.311| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31592 Z= 0.149 Angle : 0.920 15.355 42888 Z= 0.431 Chirality : 0.051 0.245 4888 Planarity : 0.005 0.090 5328 Dihedral : 12.530 140.101 4667 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 6.33 % Allowed : 34.21 % Favored : 59.46 % 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: -2.18 (0.13), residues: 3880 helix: -1.33 (0.14), residues: 1224 sheet: -2.29 (0.19), residues: 576 loop : -1.17 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 407 TYR 0.031 0.002 TYR B 509 PHE 0.015 0.001 PHE A 402 HIS 0.006 0.001 HIS D 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (31576) covalent geometry : angle 0.91951 / 0.43 (42888) hydrogen bonds : bond 0.03583 / 2.31 ( 832) hydrogen bonds : angle 5.28489 / 3.63 ( 2376) Misc. bond : bond 0.00038 / 0.02 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1276 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 1074 time to evaluate : 1.012 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: A 13 VAL cc_start: 0.8093 (t) cc_final: 0.7877 (t) REVERT: A 51 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7994 (pp) REVERT: A 111 GLU cc_start: 0.8730 (mp0) cc_final: 0.8224 (pm20) REVERT: A 128 ARG cc_start: 0.8579 (mmt90) cc_final: 0.8262 (mmt180) REVERT: A 166 LEU cc_start: 0.7945 (tp) cc_final: 0.7739 (tp) REVERT: A 186 VAL cc_start: 0.9441 (m) cc_final: 0.9124 (m) REVERT: A 206 LYS cc_start: 0.8300 (mtmt) cc_final: 0.7799 (ttpt) REVERT: A 216 ASP cc_start: 0.8998 (t70) cc_final: 0.8704 (t0) REVERT: A 250 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7850 (pp) REVERT: A 261 ASP cc_start: 0.8906 (t0) cc_final: 0.8649 (m-30) REVERT: A 297 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8650 (tm) REVERT: A 311 LYS cc_start: 0.8706 (tmtt) cc_final: 0.8318 (ttpp) REVERT: A 337 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7001 (tt) REVERT: A 386 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8533 (pmm) REVERT: A 420 MET cc_start: 0.7223 (mmm) cc_final: 0.6738 (mmm) REVERT: A 469 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.7693 (pt0) REVERT: A 470 ASP cc_start: 0.8601 (m-30) cc_final: 0.8331 (m-30) REVERT: A 490 PHE cc_start: 0.8375 (m-80) cc_final: 0.8018 (m-80) REVERT: B 47 ASP cc_start: 0.8997 (m-30) cc_final: 0.8259 (p0) REVERT: B 109 LYS cc_start: 0.8714 (mmtm) cc_final: 0.8511 (mptt) REVERT: B 111 GLU cc_start: 0.8644 (mp0) cc_final: 0.8117 (pm20) REVERT: B 128 ARG cc_start: 0.9001 (mmm-85) cc_final: 0.8634 (mmt90) REVERT: B 165 PHE cc_start: 0.7856 (p90) cc_final: 0.7558 (p90) REVERT: B 166 LEU cc_start: 0.8213 (tp) cc_final: 0.7927 (tp) REVERT: B 202 GLN cc_start: 0.9342 (mm-40) cc_final: 0.9059 (mm-40) REVERT: B 206 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7969 (ttpt) REVERT: B 216 ASP cc_start: 0.8858 (t70) cc_final: 0.8528 (t0) REVERT: B 258 TYR cc_start: 0.7782 (t80) cc_final: 0.7563 (t80) REVERT: B 311 LYS cc_start: 0.8738 (tmtt) cc_final: 0.8230 (tmtt) REVERT: B 337 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7098 (tt) REVERT: B 420 MET cc_start: 0.7398 (mmm) cc_final: 0.6753 (mmm) REVERT: B 469 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7334 (pt0) REVERT: B 470 ASP cc_start: 0.8685 (m-30) cc_final: 0.8266 (m-30) REVERT: B 490 PHE cc_start: 0.8458 (m-80) cc_final: 0.8188 (m-80) REVERT: C 32 TYR cc_start: 0.8521 (m-10) cc_final: 0.8279 (m-10) REVERT: C 78 MET cc_start: 0.7077 (ttt) cc_final: 0.6623 (ttt) REVERT: C 90 PHE cc_start: 0.7739 (m-10) cc_final: 0.6939 (m-10) REVERT: C 128 ARG cc_start: 0.8962 (mmm-85) cc_final: 0.8658 (mmt90) REVERT: C 165 PHE cc_start: 0.8187 (p90) cc_final: 0.6976 (p90) REVERT: C 166 LEU cc_start: 0.8123 (tp) cc_final: 0.7851 (tp) REVERT: C 199 GLU cc_start: 0.9499 (tp30) cc_final: 0.9225 (tp30) REVERT: C 202 GLN cc_start: 0.9348 (mm-40) cc_final: 0.8526 (mm-40) REVERT: C 214 GLU cc_start: 0.9270 (mm-30) cc_final: 0.8995 (mp0) REVERT: C 216 ASP cc_start: 0.9052 (t70) cc_final: 0.8682 (t0) REVERT: C 235 LEU cc_start: 0.9038 (mt) cc_final: 0.8782 (mt) REVERT: C 297 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8703 (tm) REVERT: C 311 LYS cc_start: 0.8657 (tmtt) cc_final: 0.8283 (ttpp) REVERT: C 337 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7015 (tt) REVERT: C 352 GLU cc_start: 0.8727 (tp30) cc_final: 0.8441 (tp30) REVERT: C 386 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8259 (pmm) REVERT: C 420 MET cc_start: 0.7364 (mmm) cc_final: 0.6883 (mmm) REVERT: C 490 PHE cc_start: 0.8361 (m-80) cc_final: 0.8104 (m-80) REVERT: D 32 TYR cc_start: 0.8572 (m-10) cc_final: 0.8347 (m-10) REVERT: D 51 LEU cc_start: 0.8323 (mm) cc_final: 0.8023 (mt) REVERT: D 109 LYS cc_start: 0.8644 (mmtm) cc_final: 0.8400 (mptt) REVERT: D 111 GLU cc_start: 0.8771 (mp0) cc_final: 0.8559 (mp0) REVERT: D 128 ARG cc_start: 0.8822 (mmt90) cc_final: 0.8412 (mmt180) REVERT: D 150 MET cc_start: 0.8967 (tmm) cc_final: 0.8446 (tpt) REVERT: D 165 PHE cc_start: 0.7907 (p90) cc_final: 0.7557 (p90) REVERT: D 179 MET cc_start: 0.7878 (mtm) cc_final: 0.7277 (pmm) REVERT: D 199 GLU cc_start: 0.9418 (tp30) cc_final: 0.8998 (tp30) REVERT: D 202 GLN cc_start: 0.9348 (mm-40) cc_final: 0.8927 (mm-40) REVERT: D 203 ARG cc_start: 0.9326 (ptp-110) cc_final: 0.9054 (ptp-110) REVERT: D 206 LYS cc_start: 0.8456 (mtmt) cc_final: 0.8078 (ttpt) REVERT: D 216 ASP cc_start: 0.9026 (t70) cc_final: 0.8658 (t0) REVERT: D 261 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8189 (p0) REVERT: D 311 LYS cc_start: 0.8624 (tmtt) cc_final: 0.8148 (tmtt) REVERT: D 361 VAL cc_start: 0.9385 (t) cc_final: 0.9151 (m) REVERT: D 386 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8271 (pmm) REVERT: D 400 TYR cc_start: 0.7723 (m-80) cc_final: 0.7279 (m-80) REVERT: D 407 ARG cc_start: 0.7272 (ttt180) cc_final: 0.6658 (ttt180) REVERT: D 420 MET cc_start: 0.7383 (mmm) cc_final: 0.6769 (mmm) REVERT: D 459 TYR cc_start: 0.8898 (t80) cc_final: 0.8615 (t80) REVERT: D 469 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.7730 (pt0) REVERT: D 470 ASP cc_start: 0.8628 (m-30) cc_final: 0.8263 (m-30) REVERT: D 488 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7106 (tt) REVERT: D 490 PHE cc_start: 0.8365 (m-80) cc_final: 0.7779 (m-80) REVERT: D 510 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6997 (mm-30) REVERT: E 78 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7656 (ttt) REVERT: E 90 PHE cc_start: 0.7695 (m-10) cc_final: 0.6985 (m-10) REVERT: E 132 GLU cc_start: 0.9480 (mp0) cc_final: 0.9114 (mp0) REVERT: E 165 PHE cc_start: 0.8090 (p90) cc_final: 0.7814 (p90) REVERT: E 166 LEU cc_start: 0.8083 (tp) cc_final: 0.7794 (tp) REVERT: E 185 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7572 (mt) REVERT: E 206 LYS cc_start: 0.8481 (tppt) cc_final: 0.8037 (tppt) REVERT: E 216 ASP cc_start: 0.9151 (t70) cc_final: 0.8788 (t0) REVERT: E 262 LEU cc_start: 0.9308 (tp) cc_final: 0.9021 (tp) REVERT: E 297 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8744 (tm) REVERT: E 311 LYS cc_start: 0.8679 (tmtt) cc_final: 0.8302 (ttpp) REVERT: E 337 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.6920 (tt) REVERT: E 386 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8286 (pmm) REVERT: E 400 TYR cc_start: 0.7547 (m-80) cc_final: 0.7260 (m-80) REVERT: E 407 ARG cc_start: 0.6781 (ttt90) cc_final: 0.6315 (ttt180) REVERT: E 420 MET cc_start: 0.7435 (mmm) cc_final: 0.6702 (mmm) REVERT: E 470 ASP cc_start: 0.8649 (m-30) cc_final: 0.8351 (m-30) REVERT: E 490 PHE cc_start: 0.8417 (m-80) cc_final: 0.8064 (m-80) REVERT: E 509 TYR cc_start: 0.7431 (p90) cc_final: 0.7059 (p90) REVERT: F 32 TYR cc_start: 0.8610 (m-10) cc_final: 0.8267 (m-10) REVERT: F 47 ASP cc_start: 0.9147 (m-30) cc_final: 0.8339 (p0) REVERT: F 59 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7671 (pt) REVERT: F 62 LYS cc_start: 0.9179 (mmtp) cc_final: 0.8912 (mttm) REVERT: F 78 MET cc_start: 0.7866 (ttm) cc_final: 0.7551 (ttt) REVERT: F 109 LYS cc_start: 0.8660 (mmtm) cc_final: 0.8420 (mptt) REVERT: F 111 GLU cc_start: 0.8791 (mp0) cc_final: 0.8217 (pm20) REVERT: F 161 ARG cc_start: 0.9558 (mpp-170) cc_final: 0.9213 (mpt-90) REVERT: F 165 PHE cc_start: 0.8372 (p90) cc_final: 0.8013 (p90) REVERT: F 166 LEU cc_start: 0.8229 (tp) cc_final: 0.7908 (tp) REVERT: F 199 GLU cc_start: 0.9515 (tp30) cc_final: 0.9180 (tp30) REVERT: F 203 ARG cc_start: 0.9278 (ptp-110) cc_final: 0.9000 (ptp-110) REVERT: F 216 ASP cc_start: 0.9072 (t70) cc_final: 0.8708 (t0) REVERT: F 261 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.8267 (p0) REVERT: F 297 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8779 (tm) REVERT: F 311 LYS cc_start: 0.8740 (tmtt) cc_final: 0.8272 (tmtt) REVERT: F 337 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7151 (tt) REVERT: F 361 VAL cc_start: 0.9504 (t) cc_final: 0.9211 (m) REVERT: F 379 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9090 (tm) REVERT: F 386 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8094 (pmm) REVERT: F 399 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8184 (tm-30) REVERT: F 470 ASP cc_start: 0.8545 (m-30) cc_final: 0.8136 (m-30) REVERT: F 490 PHE cc_start: 0.8441 (m-80) cc_final: 0.8198 (m-80) REVERT: F 509 TYR cc_start: 0.7350 (p90) cc_final: 0.7002 (p90) REVERT: F 510 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6840 (mm-30) REVERT: G 32 TYR cc_start: 0.8412 (m-10) cc_final: 0.8188 (m-10) REVERT: G 66 VAL cc_start: 0.8963 (p) cc_final: 0.8606 (p) REVERT: G 150 MET cc_start: 0.9010 (tmm) cc_final: 0.8545 (tpt) REVERT: G 165 PHE cc_start: 0.8026 (p90) cc_final: 0.7540 (p90) REVERT: G 166 LEU cc_start: 0.8075 (tp) cc_final: 0.7806 (tp) REVERT: G 199 GLU cc_start: 0.9510 (tp30) cc_final: 0.9091 (tp30) REVERT: G 206 LYS cc_start: 0.8594 (mtmt) cc_final: 0.8093 (ttpt) REVERT: G 216 ASP cc_start: 0.9114 (t70) cc_final: 0.8824 (t0) REVERT: G 297 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8648 (tm) REVERT: G 311 LYS cc_start: 0.8659 (tmtt) cc_final: 0.8292 (ttpp) REVERT: G 337 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7002 (tt) REVERT: G 352 GLU cc_start: 0.8800 (tp30) cc_final: 0.8465 (tp30) REVERT: G 386 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8476 (pmm) REVERT: G 420 MET cc_start: 0.7176 (mmm) cc_final: 0.6607 (mmm) REVERT: G 466 HIS cc_start: 0.8523 (OUTLIER) cc_final: 0.7809 (t-90) REVERT: G 469 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.7586 (pt0) REVERT: G 470 ASP cc_start: 0.8588 (m-30) cc_final: 0.8216 (m-30) REVERT: G 490 PHE cc_start: 0.8385 (m-80) cc_final: 0.7983 (m-80) REVERT: H 47 ASP cc_start: 0.9016 (m-30) cc_final: 0.8171 (p0) REVERT: H 62 LYS cc_start: 0.9263 (mmtp) cc_final: 0.8814 (mtpt) REVERT: H 78 MET cc_start: 0.7372 (ttt) cc_final: 0.7138 (tmm) REVERT: H 128 ARG cc_start: 0.8911 (mmm-85) cc_final: 0.8674 (mmt90) REVERT: H 161 ARG cc_start: 0.9551 (mpp-170) cc_final: 0.9144 (mpt-90) REVERT: H 165 PHE cc_start: 0.7983 (p90) cc_final: 0.7355 (p90) REVERT: H 166 LEU cc_start: 0.8211 (tp) cc_final: 0.7919 (tp) REVERT: H 199 GLU cc_start: 0.9456 (tp30) cc_final: 0.8691 (tp30) REVERT: H 202 GLN cc_start: 0.9393 (mm-40) cc_final: 0.8429 (pp30) REVERT: H 203 ARG cc_start: 0.9308 (ptp-110) cc_final: 0.8706 (ptp-110) REVERT: H 206 LYS cc_start: 0.8535 (mtmt) cc_final: 0.8036 (ttpt) REVERT: H 216 ASP cc_start: 0.8971 (t70) cc_final: 0.8661 (t0) REVERT: H 250 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7632 (pp) REVERT: H 297 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8780 (tm) REVERT: H 311 LYS cc_start: 0.8685 (tmtt) cc_final: 0.8215 (tmtt) REVERT: H 361 VAL cc_start: 0.9388 (t) cc_final: 0.8992 (m) REVERT: H 386 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8152 (pmm) REVERT: H 470 ASP cc_start: 0.8696 (m-30) cc_final: 0.8304 (m-30) REVERT: H 490 PHE cc_start: 0.8454 (m-80) cc_final: 0.7921 (m-80) REVERT: H 509 TYR cc_start: 0.7533 (p90) cc_final: 0.7198 (p90) outliers start: 202 outliers final: 144 residues processed: 1163 average time/residue: 0.1813 time to fit residues: 344.9489 Evaluate side-chains 1187 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 1006 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 222 ILE Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 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 120 VAL Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 510 GLU 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 78 MET Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 120 VAL 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 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 337 LEU Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 59 ILE 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 186 VAL 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 297 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain 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 73 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 337 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 466 HIS Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 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 284 ILE Chi-restraints excluded: chain H residue 294 TYR 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 351 SER Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 494 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 56 optimal weight: 2.9990 chunk 273 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 314 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 377 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 214 optimal weight: 4.9990 chunk 235 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 GLN ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 HIS ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 GLN F 368 GLN F 469 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 GLN H 298 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 469 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.163323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.127267 restraints weight = 52087.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.132698 restraints weight = 30122.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.136501 restraints weight = 20533.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.139181 restraints weight = 15432.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.141097 restraints weight = 12415.289| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 31592 Z= 0.195 Angle : 0.930 12.660 42888 Z= 0.444 Chirality : 0.051 0.256 4888 Planarity : 0.006 0.092 5328 Dihedral : 12.250 138.925 4655 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 6.45 % Allowed : 34.74 % Favored : 58.80 % 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: -2.30 (0.13), residues: 3880 helix: -1.53 (0.13), residues: 1280 sheet: -2.29 (0.19), residues: 576 loop : -1.17 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 407 TYR 0.030 0.003 TYR D 509 PHE 0.020 0.001 PHE E 90 HIS 0.006 0.001 HIS G 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (31576) covalent geometry : angle 0.92994 / 0.44 (42888) hydrogen bonds : bond 0.03675 / 2.40 ( 832) hydrogen bonds : angle 5.33459 / 3.66 ( 2376) Misc. bond : bond 0.00041 / 0.03 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7120.81 seconds wall clock time: 123 minutes 43.32 seconds (7423.32 seconds total)