Starting phenix.real_space_refine on Mon Dec 30 04:53:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rgq_24454/12_2024/7rgq_24454_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rgq_24454/12_2024/7rgq_24454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rgq_24454/12_2024/7rgq_24454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rgq_24454/12_2024/7rgq_24454.map" model { file = "/net/cci-nas-00/data/ceres_data/7rgq_24454/12_2024/7rgq_24454_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rgq_24454/12_2024/7rgq_24454_trim.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.000 sd= 0.500 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 96 5.49 5 S 184 5.16 5 C 18840 2.51 5 N 5160 2.21 5 O 6008 1.98 5 H 29544 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 276 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 59832 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 7317 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 18, 'TRANS': 462} Chain breaks: 2 Chain: "B" Number of atoms: 7317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 7317 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 18, 'TRANS': 462} Chain breaks: 2 Chain: "C" Number of atoms: 7317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 7317 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 18, 'TRANS': 462} Chain breaks: 2 Chain: "D" Number of atoms: 7317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 7317 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 18, 'TRANS': 462} Chain breaks: 2 Chain: "E" Number of atoms: 7317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 7317 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 18, 'TRANS': 462} Chain breaks: 2 Chain: "F" Number of atoms: 7317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 7317 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 18, 'TRANS': 462} Chain breaks: 2 Chain: "G" Number of atoms: 7317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 7317 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 18, 'TRANS': 462} Chain breaks: 2 Chain: "H" Number of atoms: 7317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 7317 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 18, 'TRANS': 462} Chain breaks: 2 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Time building chain proxies: 23.82, per 1000 atoms: 0.40 Number of scatterers: 59832 At special positions: 0 Unit cell: (151.96, 151.96, 114.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 184 16.00 P 96 15.00 O 6008 8.00 N 5160 7.00 C 18840 6.00 H 29544 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.21 Conformation dependent library (CDL) restraints added in 4.1 seconds 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6912 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 46 sheets defined 38.5% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.07 Creating SS restraints... Processing helix chain 'A' and resid 19 through 24 removed outlier: 3.632A pdb=" N LEU A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 19 through 24' Processing helix chain 'A' and resid 75 through 84 removed outlier: 3.695A pdb=" N ALA A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.740A pdb=" N VAL A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 195 through 203 removed outlier: 3.617A pdb=" N GLU A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.970A pdb=" N LEU A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 266 removed outlier: 4.238A pdb=" N ASP A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 317 removed outlier: 4.845A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 342 through 355 removed outlier: 3.591A pdb=" N TYR A 348 " --> pdb=" O GLY A 344 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 Processing helix chain 'A' and resid 414 through 417 removed outlier: 4.117A pdb=" N LEU A 417 " --> pdb=" O MET A 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 414 through 417' Processing helix chain 'A' and resid 452 through 472 Proline residue: A 458 - end of helix removed outlier: 3.602A pdb=" N HIS A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP A 470 " --> pdb=" O HIS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'B' and resid 19 through 24 removed outlier: 3.631A pdb=" N LEU B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 19 through 24' Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 75 through 84 removed outlier: 3.705A pdb=" N ALA B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 126 through 138 removed outlier: 3.736A pdb=" N VAL B 130 " --> pdb=" O THR B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 195 through 203 Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'B' and resid 255 through 266 removed outlier: 3.592A pdb=" N ARG B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 262 " --> pdb=" O TYR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 317 removed outlier: 4.961A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 342 through 356 removed outlier: 3.590A pdb=" N TYR B 348 " --> pdb=" O GLY B 344 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 378 Processing helix chain 'B' and resid 452 through 472 Proline residue: B 458 - end of helix removed outlier: 3.550A pdb=" N HIS B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP B 470 " --> pdb=" O HIS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 499 removed outlier: 3.679A pdb=" N ILE B 499 " --> pdb=" O MET B 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 24 removed outlier: 3.628A pdb=" N LEU C 23 " --> pdb=" O THR C 19 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 19 through 24' Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 75 through 84 removed outlier: 3.731A pdb=" N ALA C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 126 through 138 removed outlier: 3.705A pdb=" N VAL C 130 " --> pdb=" O THR C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 195 through 203 removed outlier: 3.618A pdb=" N GLU C 199 " --> pdb=" O LYS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 233 removed outlier: 3.963A pdb=" N LEU C 227 " --> pdb=" O ALA C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 266 removed outlier: 3.573A pdb=" N ARG C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 262 " --> pdb=" O TYR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 317 removed outlier: 4.970A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 338 Processing helix chain 'C' and resid 342 through 355 removed outlier: 3.590A pdb=" N TYR C 348 " --> pdb=" O GLY C 344 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 378 Processing helix chain 'C' and resid 452 through 472 Proline residue: C 458 - end of helix removed outlier: 3.552A pdb=" N HIS C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP C 470 " --> pdb=" O HIS C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 494 through 499 removed outlier: 3.729A pdb=" N ILE C 499 " --> pdb=" O MET C 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 24 removed outlier: 3.640A pdb=" N LEU D 23 " --> pdb=" O THR D 19 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 19 through 24' Processing helix chain 'D' and resid 31 through 35 removed outlier: 3.952A pdb=" N PHE D 35 " --> pdb=" O TYR D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 84 removed outlier: 3.681A pdb=" N ALA D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 126 through 138 removed outlier: 3.898A pdb=" N VAL D 130 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 195 through 203 removed outlier: 3.618A pdb=" N GLU D 199 " --> pdb=" O LYS D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 233 removed outlier: 4.014A pdb=" N LEU D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 266 removed outlier: 3.600A pdb=" N ARG D 259 " --> pdb=" O ASP D 255 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU D 262 " --> pdb=" O TYR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 317 removed outlier: 4.838A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 342 through 355 removed outlier: 3.591A pdb=" N TYR D 348 " --> pdb=" O GLY D 344 " (cutoff:3.500A) removed outlier: 4.343A 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 369 through 378 removed outlier: 3.560A pdb=" N VAL D 373 " --> pdb=" O THR D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 472 Proline residue: D 458 - end of helix removed outlier: 3.937A pdb=" N ASP D 470 " --> pdb=" O HIS D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 498 Processing helix chain 'E' and resid 19 through 24 removed outlier: 3.634A pdb=" N LEU E 23 " --> pdb=" O THR E 19 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE E 24 " --> pdb=" O ALA E 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 19 through 24' Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 75 through 84 removed outlier: 3.728A pdb=" N ALA E 79 " --> pdb=" O GLU E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 126 through 138 removed outlier: 3.912A pdb=" N VAL E 130 " --> pdb=" O THR E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 163 Processing helix chain 'E' and resid 174 through 178 Processing helix chain 'E' and resid 195 through 203 removed outlier: 3.617A pdb=" N GLU E 199 " --> pdb=" O LYS E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 233 removed outlier: 4.019A pdb=" N LEU E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 266 removed outlier: 3.645A pdb=" N ARG E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP E 261 " --> pdb=" O LYS E 257 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU E 262 " --> pdb=" O TYR E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 317 removed outlier: 4.917A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 342 through 355 removed outlier: 3.590A pdb=" N TYR E 348 " --> pdb=" O GLY E 344 " (cutoff:3.500A) removed outlier: 4.343A 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 369 through 378 removed outlier: 3.609A pdb=" N VAL E 373 " --> pdb=" O THR E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 472 Proline residue: E 458 - end of helix removed outlier: 3.607A pdb=" N HIS E 466 " --> pdb=" O ALA E 462 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP E 470 " --> pdb=" O HIS E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 494 through 499 removed outlier: 3.639A pdb=" N ILE E 499 " --> pdb=" O MET E 495 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 24 removed outlier: 3.629A pdb=" N LEU F 23 " --> pdb=" O THR F 19 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 19 through 24' Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 75 through 84 removed outlier: 3.709A pdb=" N ALA F 79 " --> pdb=" O GLU F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 126 through 138 removed outlier: 3.842A pdb=" N VAL F 130 " --> pdb=" O THR F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 174 through 178 removed outlier: 4.112A pdb=" N GLU F 177 " --> pdb=" O LEU F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 205 Processing helix chain 'F' and resid 224 through 233 Processing helix chain 'F' and resid 255 through 266 removed outlier: 4.166A pdb=" N ARG F 259 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASP F 261 " --> pdb=" O LYS F 257 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU F 262 " --> pdb=" O TYR F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 317 removed outlier: 4.968A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 342 through 355 removed outlier: 3.590A pdb=" N TYR F 348 " --> pdb=" O GLY F 344 " (cutoff:3.500A) removed outlier: 4.343A 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 369 through 378 removed outlier: 3.504A pdb=" N VAL F 373 " --> pdb=" O THR F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 417 removed outlier: 4.287A pdb=" N LEU F 417 " --> pdb=" O MET F 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 414 through 417' Processing helix chain 'F' and resid 452 through 472 Proline residue: F 458 - end of helix removed outlier: 3.562A pdb=" N HIS F 466 " --> pdb=" O ALA F 462 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP F 470 " --> pdb=" O HIS F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 494 through 499 removed outlier: 3.693A pdb=" N ILE F 499 " --> pdb=" O MET F 495 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 24 removed outlier: 3.629A pdb=" N LEU G 23 " --> pdb=" O THR G 19 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 19 through 24' Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 75 through 84 removed outlier: 3.704A pdb=" N ALA G 79 " --> pdb=" O GLU G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'G' and resid 126 through 138 removed outlier: 3.729A pdb=" N VAL G 130 " --> pdb=" O THR G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 163 removed outlier: 3.811A pdb=" N ILE G 163 " --> pdb=" O SER G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 204 Processing helix chain 'G' and resid 224 through 233 Processing helix chain 'G' and resid 255 through 266 removed outlier: 4.165A pdb=" N ARG G 259 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU G 260 " --> pdb=" O ASP G 256 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASP G 261 " --> pdb=" O LYS G 257 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU G 262 " --> pdb=" O TYR G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 317 removed outlier: 4.996A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 338 Processing helix chain 'G' and resid 342 through 355 removed outlier: 3.591A pdb=" N TYR G 348 " --> pdb=" O GLY G 344 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 378 Processing helix chain 'G' and resid 452 through 472 Proline residue: G 458 - end of helix removed outlier: 3.537A pdb=" N HIS G 466 " --> pdb=" O ALA G 462 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY G 467 " --> pdb=" O GLY G 463 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP G 470 " --> pdb=" O HIS G 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'G' and resid 494 through 499 removed outlier: 3.583A pdb=" N ILE G 499 " --> pdb=" O MET G 495 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 24 removed outlier: 3.640A pdb=" N LEU H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 19 through 24' Processing helix chain 'H' and resid 31 through 35 removed outlier: 3.993A pdb=" N PHE H 35 " --> pdb=" O TYR H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 84 removed outlier: 3.707A pdb=" N ALA H 79 " --> pdb=" O GLU H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 109 Processing helix chain 'H' and resid 126 through 138 removed outlier: 3.640A pdb=" N VAL H 130 " --> pdb=" O THR H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 163 Processing helix chain 'H' and resid 195 through 204 Processing helix chain 'H' and resid 224 through 233 Processing helix chain 'H' and resid 255 through 266 removed outlier: 3.657A pdb=" N ARG H 259 " --> pdb=" O ASP H 255 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP H 261 " --> pdb=" O LYS H 257 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU H 262 " --> pdb=" O TYR H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 317 removed outlier: 4.976A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 338 Processing helix chain 'H' and resid 342 through 355 removed outlier: 3.591A pdb=" N TYR H 348 " --> pdb=" O GLY H 344 " (cutoff:3.500A) removed outlier: 4.342A 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 369 through 378 removed outlier: 3.610A pdb=" N VAL H 373 " --> pdb=" O THR H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 472 Proline residue: H 458 - end of helix removed outlier: 3.535A pdb=" N HIS H 466 " --> pdb=" O ALA H 462 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP H 470 " --> pdb=" O HIS H 466 " (cutoff:3.500A) Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 494 through 498 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 56 removed outlier: 6.817A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 3.656A pdb=" N ILE A 88 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP A 364 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A 383 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 145 Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 189 removed outlier: 6.096A pdb=" N ALA A 188 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 220 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 408 through 412 removed outlier: 4.070A pdb=" N SER B 508 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 508 through 510 removed outlier: 4.004A pdb=" N SER A 508 " --> pdb=" O SER D 446 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 56 removed outlier: 6.930A pdb=" N ILE B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 66 through 67 removed outlier: 3.858A pdb=" N PHE B 90 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 141 through 145 removed outlier: 3.633A pdb=" N GLY B 156 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 157 " --> pdb=" O THR B 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 188 through 189 removed outlier: 3.542A pdb=" N ALA B 220 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 400 through 402 removed outlier: 3.992A pdb=" N SER C 508 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 35 through 37 removed outlier: 3.505A pdb=" N GLU C 491 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 56 removed outlier: 6.930A pdb=" N ILE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.652A pdb=" N ILE C 88 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE C 90 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ARG C 322 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP C 364 " --> pdb=" O VAL C 323 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR C 383 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE C 66 " --> pdb=" O MET C 386 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 143 through 145 removed outlier: 3.529A pdb=" N GLY C 156 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE C 157 " --> pdb=" O THR C 180 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 188 through 189 removed outlier: 5.990A pdb=" N ALA C 188 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA C 220 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 400 through 402 removed outlier: 3.690A pdb=" N LEU C 408 " --> pdb=" O PHE C 401 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER D 508 " --> pdb=" O SER C 446 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 56 removed outlier: 6.891A pdb=" N ILE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 65 through 67 removed outlier: 3.602A pdb=" N ILE D 88 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE D 90 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL D 299 " --> pdb=" O GLY D 320 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ARG D 322 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY D 301 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N MET D 385 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE D 66 " --> pdb=" O MET D 386 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 142 through 145 removed outlier: 3.555A pdb=" N GLY D 156 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 188 through 189 removed outlier: 6.035A pdb=" N ALA D 188 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA D 220 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AC7, first strand: chain 'E' and resid 53 through 56 removed outlier: 6.925A pdb=" N ILE E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 66 through 67 removed outlier: 3.874A pdb=" N PHE E 90 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLY E 89 " --> pdb=" O GLY E 247 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ALA E 249 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE E 91 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE E 271 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N GLY E 302 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU E 273 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N VAL E 304 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ASP E 364 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL E 323 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 142 through 145 removed outlier: 3.536A pdb=" N GLY E 156 " --> pdb=" O ILE E 144 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 188 through 189 removed outlier: 6.012A pdb=" N ALA E 188 " --> pdb=" O VAL E 212 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA E 220 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 400 through 401 removed outlier: 3.661A pdb=" N LEU E 408 " --> pdb=" O PHE E 401 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER F 508 " --> pdb=" O SER E 446 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 508 through 510 removed outlier: 3.992A pdb=" N SER E 508 " --> pdb=" O SER H 446 " (cutoff:3.500A) 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 56 removed outlier: 6.898A pdb=" N ILE F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 66 through 67 removed outlier: 3.832A pdb=" N PHE F 90 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 142 through 145 Processing sheet with id=AD8, first strand: chain 'F' and resid 188 through 189 Processing sheet with id=AD9, first strand: chain 'F' and resid 400 through 401 removed outlier: 3.617A pdb=" N LEU F 408 " --> pdb=" O PHE F 401 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER G 508 " --> pdb=" O SER F 446 " (cutoff:3.500A) 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 56 removed outlier: 6.900A pdb=" N ILE G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 65 through 67 removed outlier: 3.656A pdb=" N ILE G 88 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE G 90 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY G 89 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ALA G 249 " --> pdb=" O GLY G 89 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE G 91 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP G 364 " --> pdb=" O VAL G 323 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR G 383 " --> pdb=" O ILE G 361 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 142 through 145 Processing sheet with id=AE5, first strand: chain 'G' and resid 188 through 189 Processing sheet with id=AE6, first strand: chain 'G' and resid 400 through 402 removed outlier: 3.606A pdb=" N LEU G 408 " --> pdb=" O PHE G 401 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER H 508 " --> pdb=" O SER G 446 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 53 through 56 removed outlier: 6.870A pdb=" N ILE H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 65 through 67 removed outlier: 3.748A pdb=" N ILE H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE H 90 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ARG H 322 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY H 301 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N MET H 385 " --> pdb=" O ILE H 361 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE H 66 " --> pdb=" O MET H 386 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 142 through 145 removed outlier: 3.578A pdb=" N GLY H 156 " --> pdb=" O ILE H 144 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE H 157 " --> pdb=" O THR H 180 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 188 through 189 1027 hydrogen bonds defined for protein. 2862 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: 25.74 Time building geometry restraints manager: 15.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.87 - 1.06: 6339 1.06 - 1.25: 27564 1.25 - 1.44: 8324 1.44 - 1.63: 17833 1.63 - 1.82: 324 Bond restraints: 60384 Sorted by residual: bond pdb=" C2' GTP D 601 " pdb=" C3' GTP D 601 " ideal model delta sigma weight residual 1.524 1.226 0.298 2.00e-02 2.50e+03 2.21e+02 bond pdb=" C2' GTP E 601 " pdb=" C3' GTP E 601 " ideal model delta sigma weight residual 1.524 1.227 0.297 2.00e-02 2.50e+03 2.21e+02 bond pdb=" C1' GTP D 601 " pdb=" N9 GTP D 601 " ideal model delta sigma weight residual 1.475 1.323 0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" C1' GTP E 601 " pdb=" N9 GTP E 601 " ideal model delta sigma weight residual 1.475 1.323 0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" N ILE H 330 " pdb=" H ILE H 330 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 ... (remaining 60379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.75: 99982 3.75 - 7.50: 8637 7.50 - 11.25: 469 11.25 - 15.00: 38 15.00 - 18.76: 18 Bond angle restraints: 109144 Sorted by residual: angle pdb=" PB ATP E 604 " pdb=" O3B ATP E 604 " pdb=" PG ATP E 604 " 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 F 604 " pdb=" O3B ATP F 604 " pdb=" PG ATP F 604 " ideal model delta sigma weight residual 139.87 121.37 18.50 1.00e+00 1.00e+00 3.42e+02 angle pdb=" PA ATP B 604 " pdb=" O3A ATP B 604 " pdb=" PB ATP B 604 " ideal model delta sigma weight residual 136.83 118.51 18.32 1.00e+00 1.00e+00 3.36e+02 angle pdb=" PB ATP D 604 " pdb=" O3B ATP D 604 " pdb=" PG ATP D 604 " ideal model delta sigma weight residual 139.87 121.64 18.23 1.00e+00 1.00e+00 3.32e+02 angle pdb=" PB ATP H 604 " pdb=" O3B ATP H 604 " pdb=" PG ATP H 604 " ideal model delta sigma weight residual 139.87 121.65 18.22 1.00e+00 1.00e+00 3.32e+02 ... (remaining 109139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.80: 26410 29.80 - 59.60: 1689 59.60 - 89.40: 433 89.40 - 119.20: 25 119.20 - 149.00: 43 Dihedral angle restraints: 28600 sinusoidal: 16352 harmonic: 12248 Sorted by residual: dihedral pdb=" C8 GTP E 601 " pdb=" C1' GTP E 601 " pdb=" N9 GTP E 601 " pdb=" O4' GTP E 601 " ideal model delta sinusoidal sigma weight residual 104.59 -106.40 -149.00 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" C8 GTP D 601 " pdb=" C1' GTP D 601 " pdb=" N9 GTP D 601 " pdb=" O4' GTP D 601 " ideal model delta sinusoidal sigma weight residual 104.59 -106.43 -148.97 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" C4' GTP E 601 " pdb=" C5' GTP E 601 " pdb=" O5' GTP E 601 " pdb=" PA GTP E 601 " ideal model delta sinusoidal sigma weight residual 260.87 112.11 148.76 1 2.00e+01 2.50e-03 4.45e+01 ... (remaining 28597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 3596 0.102 - 0.205: 1075 0.205 - 0.307: 168 0.307 - 0.409: 16 0.409 - 0.512: 1 Chirality restraints: 4856 Sorted by residual: chirality pdb=" CA LYS F 205 " pdb=" N LYS F 205 " pdb=" C LYS F 205 " pdb=" CB LYS F 205 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.54e+00 chirality pdb=" CA THR H 172 " pdb=" N THR H 172 " pdb=" C THR H 172 " pdb=" CB THR H 172 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CA THR G 172 " pdb=" N THR G 172 " pdb=" C THR G 172 " pdb=" CB THR G 172 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.40 2.00e-01 2.50e+01 3.96e+00 ... (remaining 4853 not shown) Planarity restraints: 8840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' IMP A 603 " -0.335 2.00e-02 2.50e+03 1.55e-01 6.00e+02 pdb=" C2 IMP A 603 " 0.081 2.00e-02 2.50e+03 pdb=" C4 IMP A 603 " 0.136 2.00e-02 2.50e+03 pdb=" C5 IMP A 603 " -0.004 2.00e-02 2.50e+03 pdb=" C6 IMP A 603 " -0.193 2.00e-02 2.50e+03 pdb=" C8 IMP A 603 " 0.143 2.00e-02 2.50e+03 pdb=" N1 IMP A 603 " -0.105 2.00e-02 2.50e+03 pdb=" N3 IMP A 603 " 0.140 2.00e-02 2.50e+03 pdb=" N7 IMP A 603 " 0.019 2.00e-02 2.50e+03 pdb=" N9 IMP A 603 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 224 " 0.226 9.50e-02 1.11e+02 1.31e-01 2.65e+02 pdb=" NE ARG G 224 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG G 224 " -0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG G 224 " -0.067 2.00e-02 2.50e+03 pdb=" NH2 ARG G 224 " -0.043 2.00e-02 2.50e+03 pdb="HH11 ARG G 224 " -0.092 2.00e-02 2.50e+03 pdb="HH12 ARG G 224 " 0.232 2.00e-02 2.50e+03 pdb="HH21 ARG G 224 " 0.107 2.00e-02 2.50e+03 pdb="HH22 ARG G 224 " -0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP F 604 " -0.212 2.00e-02 2.50e+03 8.92e-02 2.19e+02 pdb=" C2 ATP F 604 " 0.039 2.00e-02 2.50e+03 pdb=" C4 ATP F 604 " 0.074 2.00e-02 2.50e+03 pdb=" C5 ATP F 604 " 0.053 2.00e-02 2.50e+03 pdb=" C6 ATP F 604 " -0.022 2.00e-02 2.50e+03 pdb=" C8 ATP F 604 " 0.059 2.00e-02 2.50e+03 pdb=" N1 ATP F 604 " -0.030 2.00e-02 2.50e+03 pdb=" N3 ATP F 604 " 0.071 2.00e-02 2.50e+03 pdb=" N6 ATP F 604 " -0.134 2.00e-02 2.50e+03 pdb=" N7 ATP F 604 " 0.054 2.00e-02 2.50e+03 pdb=" N9 ATP F 604 " 0.047 2.00e-02 2.50e+03 ... (remaining 8837 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 2657 2.12 - 2.74: 96079 2.74 - 3.36: 171800 3.36 - 3.98: 228607 3.98 - 4.60: 346694 Nonbonded interactions: 845837 Sorted by model distance: nonbonded pdb="HD21 LEU A 38 " pdb=" HD3 ARG D 341 " model vdw 1.502 2.440 nonbonded pdb=" HD3 ARG C 341 " pdb="HD21 LEU D 38 " model vdw 1.504 2.440 nonbonded pdb=" HD3 ARG B 341 " pdb="HD21 LEU C 38 " model vdw 1.504 2.440 nonbonded pdb=" HD3 ARG A 341 " pdb="HD21 LEU B 38 " model vdw 1.504 2.440 nonbonded pdb=" HD3 ARG G 341 " pdb="HD21 LEU H 38 " model vdw 1.507 2.440 ... (remaining 845832 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: 0.00 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: 2.450 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: 0.920 Extract box with map and model: 1.920 Check model and map are aligned: 0.360 Set scattering table: 0.450 Process input model: 107.050 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.250 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: 0.020 Load rotamer database and sin/cos tables:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 : 0.013 0.298 30840 Z= 0.863 Angle : 1.974 18.755 41952 Z= 1.239 Chirality : 0.094 0.512 4856 Planarity : 0.013 0.155 5160 Dihedral : 19.503 149.003 11864 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.95 % Favored : 92.39 % Rotamer: Outliers : 2.74 % Allowed : 5.29 % Favored : 91.96 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.13), residues: 3800 helix: -1.72 (0.13), residues: 1256 sheet: -1.36 (0.23), residues: 456 loop : -0.94 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS C 125 PHE 0.046 0.009 PHE A 456 TYR 0.109 0.015 TYR B 32 ARG 0.009 0.001 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1182 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 1096 time to evaluate : 3.639 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 48 GLU cc_start: 0.8461 (tp30) cc_final: 0.8084 (tp30) REVERT: A 129 ASP cc_start: 0.8555 (t0) cc_final: 0.8336 (t0) REVERT: A 135 MET cc_start: 0.7846 (ttp) cc_final: 0.7644 (tmm) REVERT: A 179 MET cc_start: 0.8501 (pp-130) cc_final: 0.8101 (pp-130) REVERT: A 204 SER cc_start: 0.8667 (t) cc_final: 0.8386 (t) REVERT: A 241 GLN cc_start: 0.8047 (mp10) cc_final: 0.7404 (mp10) REVERT: A 274 ASP cc_start: 0.8812 (t0) cc_final: 0.8609 (t0) REVERT: A 286 MET cc_start: 0.8864 (tpt) cc_final: 0.8273 (tpt) REVERT: A 330 ILE cc_start: 0.7885 (tp) cc_final: 0.7586 (tp) REVERT: A 385 MET cc_start: 0.8661 (ttm) cc_final: 0.8406 (ttm) REVERT: A 483 MET cc_start: 0.7658 (tpt) cc_final: 0.7236 (tpt) REVERT: B 78 MET cc_start: 0.8902 (ttm) cc_final: 0.8543 (tpp) REVERT: B 135 MET cc_start: 0.7680 (ttp) cc_final: 0.7450 (tmm) REVERT: B 140 SER cc_start: 0.9089 (t) cc_final: 0.8877 (t) REVERT: B 274 ASP cc_start: 0.8773 (t0) cc_final: 0.8470 (t0) REVERT: B 385 MET cc_start: 0.8757 (ttm) cc_final: 0.8306 (ttm) REVERT: B 483 MET cc_start: 0.7596 (tpt) cc_final: 0.7192 (tpt) REVERT: C 129 ASP cc_start: 0.8162 (t0) cc_final: 0.7869 (t0) REVERT: C 204 SER cc_start: 0.8761 (t) cc_final: 0.8554 (t) REVERT: C 205 LYS cc_start: 0.9198 (ptpp) cc_final: 0.8909 (pttm) REVERT: C 241 GLN cc_start: 0.8058 (mp10) cc_final: 0.7373 (mp10) REVERT: C 274 ASP cc_start: 0.8831 (t0) cc_final: 0.8532 (t0) REVERT: C 284 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.9099 (tt) REVERT: C 286 MET cc_start: 0.8887 (tpt) cc_final: 0.8241 (tpt) REVERT: C 466 HIS cc_start: 0.7897 (t-90) cc_final: 0.7656 (t-170) REVERT: C 483 MET cc_start: 0.7659 (tpt) cc_final: 0.7276 (tpt) REVERT: D 32 TYR cc_start: 0.9193 (m-80) cc_final: 0.8227 (m-80) REVERT: D 129 ASP cc_start: 0.8319 (t0) cc_final: 0.8066 (t0) REVERT: D 178 VAL cc_start: 0.8778 (m) cc_final: 0.8564 (m) REVERT: D 215 CYS cc_start: 0.7515 (t) cc_final: 0.7233 (t) REVERT: D 385 MET cc_start: 0.8671 (ttm) cc_final: 0.8061 (ttm) REVERT: D 466 HIS cc_start: 0.7943 (t-90) cc_final: 0.7551 (t-170) REVERT: D 483 MET cc_start: 0.7633 (tpt) cc_final: 0.7235 (tpt) REVERT: D 512 LEU cc_start: 0.5076 (OUTLIER) cc_final: 0.4842 (tp) REVERT: E 42 ILE cc_start: 0.9120 (mt) cc_final: 0.8857 (mt) REVERT: E 129 ASP cc_start: 0.8323 (t0) cc_final: 0.8076 (t0) REVERT: E 135 MET cc_start: 0.7777 (ttp) cc_final: 0.7517 (tmm) REVERT: E 136 ARG cc_start: 0.7166 (ttm-80) cc_final: 0.6901 (ttm-80) REVERT: E 153 LYS cc_start: 0.8218 (mtpp) cc_final: 0.7980 (mtpp) REVERT: E 215 CYS cc_start: 0.7586 (t) cc_final: 0.7259 (t) REVERT: E 241 GLN cc_start: 0.8096 (mp10) cc_final: 0.7449 (mp10) REVERT: E 274 ASP cc_start: 0.8884 (t0) cc_final: 0.8587 (t0) REVERT: E 293 LYS cc_start: 0.8591 (tttt) cc_final: 0.8377 (tppt) REVERT: E 512 LEU cc_start: 0.5123 (OUTLIER) cc_final: 0.4890 (tp) REVERT: F 58 LYS cc_start: 0.8617 (mttt) cc_final: 0.8399 (mmtp) REVERT: F 129 ASP cc_start: 0.8332 (t0) cc_final: 0.8075 (t0) REVERT: F 135 MET cc_start: 0.7746 (ttp) cc_final: 0.7538 (tmm) REVERT: F 178 VAL cc_start: 0.9029 (m) cc_final: 0.8781 (m) REVERT: F 240 SER cc_start: 0.8531 (p) cc_final: 0.8241 (p) REVERT: F 261 ASP cc_start: 0.7190 (m-30) cc_final: 0.6938 (m-30) REVERT: F 293 LYS cc_start: 0.8594 (tttt) cc_final: 0.8331 (tppt) REVERT: G 178 VAL cc_start: 0.9116 (m) cc_final: 0.8791 (m) REVERT: G 241 GLN cc_start: 0.8214 (mp10) cc_final: 0.7905 (mp10) REVERT: G 284 ILE cc_start: 0.9459 (tt) cc_final: 0.9239 (tt) REVERT: G 286 MET cc_start: 0.8858 (tpt) cc_final: 0.8291 (tpt) REVERT: H 32 TYR cc_start: 0.9198 (m-80) cc_final: 0.8261 (m-80) REVERT: H 48 GLU cc_start: 0.8417 (tp30) cc_final: 0.8062 (tp30) REVERT: H 135 MET cc_start: 0.7798 (ttp) cc_final: 0.7465 (tmm) REVERT: H 178 VAL cc_start: 0.9200 (m) cc_final: 0.8943 (m) REVERT: H 179 MET cc_start: 0.8765 (ppp) cc_final: 0.8504 (ppp) REVERT: H 286 MET cc_start: 0.8911 (tpt) cc_final: 0.8278 (tpt) REVERT: H 293 LYS cc_start: 0.8657 (tttt) cc_final: 0.8432 (tttm) REVERT: H 330 ILE cc_start: 0.8114 (tp) cc_final: 0.7812 (tp) REVERT: H 385 MET cc_start: 0.8634 (ttm) cc_final: 0.8213 (ttm) REVERT: H 466 HIS cc_start: 0.8091 (t-90) cc_final: 0.7840 (t-170) outliers start: 86 outliers final: 32 residues processed: 1160 average time/residue: 0.8349 time to fit residues: 1529.4155 Evaluate side-chains 927 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 892 time to evaluate : 3.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 395 GLU Chi-restraints excluded: chain H residue 408 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 0.8980 chunk 291 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 196 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 224 optimal weight: 0.9990 chunk 348 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS B 498 GLN F 466 HIS G 125 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30840 Z= 0.205 Angle : 0.698 8.831 41952 Z= 0.358 Chirality : 0.046 0.178 4856 Planarity : 0.005 0.049 5160 Dihedral : 20.047 157.836 5162 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.85 % Allowed : 12.60 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.13), residues: 3800 helix: -0.45 (0.15), residues: 1256 sheet: -1.39 (0.23), residues: 464 loop : -0.98 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 466 PHE 0.016 0.002 PHE A 401 TYR 0.013 0.002 TYR B 32 ARG 0.006 0.001 ARG C 161 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 981 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 923 time to evaluate : 3.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.8626 (t0) cc_final: 0.8347 (t0) REVERT: A 135 MET cc_start: 0.7869 (ttp) cc_final: 0.7589 (tmm) REVERT: A 179 MET cc_start: 0.8376 (pp-130) cc_final: 0.7886 (pp-130) REVERT: A 241 GLN cc_start: 0.8065 (mp10) cc_final: 0.7266 (mp10) REVERT: A 286 MET cc_start: 0.8743 (tpt) cc_final: 0.8181 (tpt) REVERT: A 483 MET cc_start: 0.7572 (tpt) cc_final: 0.7251 (tpt) REVERT: B 385 MET cc_start: 0.8737 (ttm) cc_final: 0.8520 (ttm) REVERT: B 483 MET cc_start: 0.7547 (tpt) cc_final: 0.7250 (tpt) REVERT: C 82 MET cc_start: 0.9170 (ttm) cc_final: 0.8873 (ttm) REVERT: C 171 HIS cc_start: 0.6796 (m90) cc_final: 0.6237 (m90) REVERT: C 241 GLN cc_start: 0.8085 (mp10) cc_final: 0.7293 (mp10) REVERT: C 261 ASP cc_start: 0.8014 (t0) cc_final: 0.7773 (t0) REVERT: C 286 MET cc_start: 0.8775 (tpt) cc_final: 0.8244 (tpp) REVERT: C 408 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7570 (pp) REVERT: C 483 MET cc_start: 0.7585 (tpt) cc_final: 0.7273 (tpt) REVERT: D 129 ASP cc_start: 0.8504 (t0) cc_final: 0.8223 (t0) REVERT: D 163 ILE cc_start: 0.9118 (mm) cc_final: 0.8898 (mm) REVERT: D 286 MET cc_start: 0.8314 (tpp) cc_final: 0.8056 (tpp) REVERT: D 408 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7386 (pp) REVERT: D 483 MET cc_start: 0.7527 (tpt) cc_final: 0.7198 (tpt) REVERT: E 129 ASP cc_start: 0.8510 (t0) cc_final: 0.8200 (t0) REVERT: E 153 LYS cc_start: 0.8145 (mtpp) cc_final: 0.7939 (mtpp) REVERT: E 241 GLN cc_start: 0.8112 (mp10) cc_final: 0.7349 (mp10) REVERT: E 408 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7847 (pp) REVERT: E 483 MET cc_start: 0.7557 (tpt) cc_final: 0.7280 (tpt) REVERT: F 129 ASP cc_start: 0.8435 (t0) cc_final: 0.8178 (t0) REVERT: F 135 MET cc_start: 0.7765 (ttp) cc_final: 0.7546 (tmm) REVERT: F 136 ARG cc_start: 0.7199 (ttm-80) cc_final: 0.6785 (ttm-80) REVERT: F 175 LEU cc_start: 0.8845 (tp) cc_final: 0.8627 (mp) REVERT: F 178 VAL cc_start: 0.8963 (m) cc_final: 0.8738 (m) REVERT: F 179 MET cc_start: 0.8595 (ppp) cc_final: 0.8386 (ppp) REVERT: F 385 MET cc_start: 0.8677 (ttm) cc_final: 0.8420 (ttm) REVERT: F 408 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7854 (pp) REVERT: F 483 MET cc_start: 0.7554 (tpt) cc_final: 0.7253 (tpt) REVERT: G 103 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8122 (mm-30) REVERT: G 175 LEU cc_start: 0.8895 (tp) cc_final: 0.8574 (mp) REVERT: G 199 GLU cc_start: 0.7367 (tp30) cc_final: 0.7001 (tp30) REVERT: G 240 SER cc_start: 0.8422 (p) cc_final: 0.8206 (p) REVERT: G 483 MET cc_start: 0.7591 (tpt) cc_final: 0.7274 (tpt) REVERT: H 32 TYR cc_start: 0.9225 (m-80) cc_final: 0.8427 (m-80) REVERT: H 135 MET cc_start: 0.7769 (ttp) cc_final: 0.7495 (tmm) REVERT: H 408 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7619 (pp) REVERT: H 483 MET cc_start: 0.7531 (tpt) cc_final: 0.7231 (tpt) outliers start: 58 outliers final: 46 residues processed: 959 average time/residue: 0.8142 time to fit residues: 1279.6633 Evaluate side-chains 900 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 849 time to evaluate : 3.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 395 GLU Chi-restraints excluded: chain H residue 408 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 290 optimal weight: 0.7980 chunk 237 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 349 optimal weight: 1.9990 chunk 377 optimal weight: 3.9990 chunk 311 optimal weight: 2.9990 chunk 346 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 280 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 466 HIS C 202 GLN C 466 HIS D 466 HIS ** G 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN H 466 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 30840 Z= 0.270 Angle : 0.638 7.488 41952 Z= 0.326 Chirality : 0.045 0.161 4856 Planarity : 0.004 0.045 5160 Dihedral : 18.608 172.110 5152 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.14 % Allowed : 13.78 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.13), residues: 3800 helix: -0.20 (0.15), residues: 1264 sheet: -1.51 (0.20), residues: 544 loop : -1.07 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS F 466 PHE 0.014 0.001 PHE B 139 TYR 0.014 0.001 TYR C 411 ARG 0.004 0.000 ARG C 161 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 950 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 883 time to evaluate : 3.614 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: A 129 ASP cc_start: 0.8661 (t0) cc_final: 0.8453 (t0) REVERT: A 135 MET cc_start: 0.7929 (ttp) cc_final: 0.7642 (tmm) REVERT: A 179 MET cc_start: 0.8307 (pp-130) cc_final: 0.7870 (pp-130) REVERT: A 261 ASP cc_start: 0.8056 (t0) cc_final: 0.7789 (t0) REVERT: A 274 ASP cc_start: 0.8900 (t0) cc_final: 0.8546 (t0) REVERT: A 286 MET cc_start: 0.8725 (tpt) cc_final: 0.8223 (tpp) REVERT: B 286 MET cc_start: 0.8552 (tpp) cc_final: 0.8181 (tpp) REVERT: C 82 MET cc_start: 0.9109 (ttm) cc_final: 0.8657 (ttm) REVERT: C 171 HIS cc_start: 0.7064 (m90) cc_final: 0.6591 (m90) REVERT: C 261 ASP cc_start: 0.8276 (t0) cc_final: 0.8000 (t0) REVERT: C 286 MET cc_start: 0.8719 (tpt) cc_final: 0.8218 (tpp) REVERT: C 408 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7633 (pp) REVERT: D 286 MET cc_start: 0.8410 (tpp) cc_final: 0.8185 (tpp) REVERT: D 300 ILE cc_start: 0.9359 (mm) cc_final: 0.8838 (mt) REVERT: D 323 VAL cc_start: 0.9771 (p) cc_final: 0.9400 (m) REVERT: D 385 MET cc_start: 0.8710 (ttm) cc_final: 0.8492 (ttm) REVERT: D 408 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7623 (pp) REVERT: E 129 ASP cc_start: 0.8523 (t0) cc_final: 0.8233 (t0) REVERT: E 153 LYS cc_start: 0.8327 (mtpp) cc_final: 0.8027 (mtpp) REVERT: E 175 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8759 (mp) REVERT: E 286 MET cc_start: 0.8302 (tpp) cc_final: 0.7968 (tpp) REVERT: F 175 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8633 (mp) REVERT: F 286 MET cc_start: 0.8615 (tpp) cc_final: 0.8197 (tpp) REVERT: F 408 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7908 (pp) REVERT: G 103 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8137 (mm-30) REVERT: G 175 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8747 (mp) REVERT: G 411 TYR cc_start: 0.8921 (t80) cc_final: 0.8639 (t80) REVERT: H 32 TYR cc_start: 0.9217 (m-80) cc_final: 0.8429 (m-80) REVERT: H 135 MET cc_start: 0.7812 (ttp) cc_final: 0.7501 (tmm) REVERT: H 153 LYS cc_start: 0.8345 (mtpp) cc_final: 0.8141 (mtpp) REVERT: H 309 GLN cc_start: 0.9280 (OUTLIER) cc_final: 0.8964 (pt0) REVERT: H 323 VAL cc_start: 0.9783 (p) cc_final: 0.9415 (m) REVERT: H 385 MET cc_start: 0.8668 (ttm) cc_final: 0.8426 (ttm) REVERT: H 408 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7730 (pp) REVERT: H 411 TYR cc_start: 0.8960 (t80) cc_final: 0.8704 (t80) outliers start: 67 outliers final: 49 residues processed: 919 average time/residue: 0.7432 time to fit residues: 1119.8371 Evaluate side-chains 895 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 838 time to evaluate : 3.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 408 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 3.9990 chunk 262 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 234 optimal weight: 0.6980 chunk 350 optimal weight: 4.9990 chunk 371 optimal weight: 2.9990 chunk 183 optimal weight: 7.9990 chunk 332 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 466 HIS C 125 HIS C 466 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 HIS G 241 GLN G 466 HIS ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 HIS H 466 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 30840 Z= 0.394 Angle : 0.660 8.028 41952 Z= 0.339 Chirality : 0.046 0.159 4856 Planarity : 0.005 0.051 5160 Dihedral : 18.187 179.045 5139 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.68 % Allowed : 15.24 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.13), residues: 3800 helix: -0.45 (0.14), residues: 1304 sheet: -1.78 (0.19), residues: 624 loop : -1.30 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 466 PHE 0.014 0.002 PHE A 41 TYR 0.011 0.001 TYR B 32 ARG 0.003 0.000 ARG D 356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 954 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 870 time to evaluate : 3.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.7972 (ttp) cc_final: 0.7737 (tmm) REVERT: A 179 MET cc_start: 0.8317 (pp-130) cc_final: 0.7898 (pp-130) REVERT: B 335 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7436 (mt-10) REVERT: C 171 HIS cc_start: 0.7181 (m90) cc_final: 0.6579 (m90) REVERT: C 284 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.9005 (tt) REVERT: C 286 MET cc_start: 0.8734 (tpt) cc_final: 0.8214 (tpp) REVERT: C 408 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7625 (pp) REVERT: D 129 ASP cc_start: 0.8427 (t0) cc_final: 0.8143 (t0) REVERT: D 205 LYS cc_start: 0.9132 (ptpp) cc_final: 0.8836 (mtmm) REVERT: D 257 LYS cc_start: 0.9150 (ttmm) cc_final: 0.8781 (mttm) REVERT: D 323 VAL cc_start: 0.9792 (p) cc_final: 0.9459 (m) REVERT: D 385 MET cc_start: 0.8830 (ttm) cc_final: 0.8621 (ttm) REVERT: D 408 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7698 (pp) REVERT: D 466 HIS cc_start: 0.8059 (t-90) cc_final: 0.7750 (t-90) REVERT: E 153 LYS cc_start: 0.8324 (mtpp) cc_final: 0.7971 (mtpp) REVERT: E 255 ASP cc_start: 0.8771 (p0) cc_final: 0.8570 (p0) REVERT: E 286 MET cc_start: 0.8273 (tpp) cc_final: 0.7919 (tpp) REVERT: F 323 VAL cc_start: 0.9760 (p) cc_final: 0.9376 (m) REVERT: F 385 MET cc_start: 0.8642 (ttm) cc_final: 0.8431 (ttm) REVERT: F 408 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7948 (pp) REVERT: F 466 HIS cc_start: 0.8319 (t-90) cc_final: 0.8095 (t-90) REVERT: G 103 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8116 (mm-30) REVERT: G 284 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.9048 (tt) REVERT: G 500 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7521 (mm-30) REVERT: H 32 TYR cc_start: 0.9210 (m-80) cc_final: 0.8425 (m-80) REVERT: H 135 MET cc_start: 0.7911 (ttp) cc_final: 0.7711 (tmm) REVERT: H 153 LYS cc_start: 0.8392 (mtpp) cc_final: 0.8144 (mtpp) REVERT: H 203 ARG cc_start: 0.7814 (ttp80) cc_final: 0.7395 (mtp-110) REVERT: H 309 GLN cc_start: 0.9401 (OUTLIER) cc_final: 0.9083 (pt0) REVERT: H 323 VAL cc_start: 0.9784 (p) cc_final: 0.9433 (m) REVERT: H 385 MET cc_start: 0.8762 (ttm) cc_final: 0.8382 (ttm) REVERT: H 411 TYR cc_start: 0.9049 (t80) cc_final: 0.8682 (t80) outliers start: 84 outliers final: 55 residues processed: 919 average time/residue: 0.7547 time to fit residues: 1141.8199 Evaluate side-chains 900 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 839 time to evaluate : 3.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 2.9990 chunk 210 optimal weight: 0.0870 chunk 5 optimal weight: 1.9990 chunk 276 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 316 optimal weight: 0.4980 chunk 256 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 333 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.5164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 466 HIS C 466 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 HIS F 125 HIS G 466 HIS ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 466 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 30840 Z= 0.251 Angle : 0.594 6.971 41952 Z= 0.302 Chirality : 0.043 0.153 4856 Planarity : 0.004 0.050 5160 Dihedral : 17.439 169.563 5136 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.39 % Allowed : 16.04 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.13), residues: 3800 helix: -0.27 (0.15), residues: 1304 sheet: -1.96 (0.18), residues: 624 loop : -1.17 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 466 PHE 0.012 0.001 PHE A 401 TYR 0.010 0.001 TYR D 400 ARG 0.002 0.000 ARG C 253 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 872 time to evaluate : 3.641 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 129 ASP cc_start: 0.8515 (t0) cc_final: 0.8273 (t0) REVERT: A 135 MET cc_start: 0.7954 (ttp) cc_final: 0.7744 (tmm) REVERT: A 179 MET cc_start: 0.8313 (pp-130) cc_final: 0.7903 (pp-130) REVERT: A 286 MET cc_start: 0.8699 (tpt) cc_final: 0.8221 (tpp) REVERT: B 78 MET cc_start: 0.9297 (tpp) cc_final: 0.9092 (tpp) REVERT: B 153 LYS cc_start: 0.8410 (mtpp) cc_final: 0.8136 (mtpp) REVERT: B 286 MET cc_start: 0.8483 (tpp) cc_final: 0.8173 (tpp) REVERT: B 323 VAL cc_start: 0.9769 (p) cc_final: 0.9372 (m) REVERT: B 364 ASP cc_start: 0.8268 (t0) cc_final: 0.8067 (t70) REVERT: C 75 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7331 (tt0) REVERT: C 171 HIS cc_start: 0.7118 (m90) cc_final: 0.6553 (m90) REVERT: C 286 MET cc_start: 0.8660 (tpt) cc_final: 0.8183 (tpp) REVERT: C 408 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7651 (pp) REVERT: D 78 MET cc_start: 0.9277 (tpp) cc_final: 0.9068 (tpp) REVERT: D 129 ASP cc_start: 0.8484 (t0) cc_final: 0.8198 (t0) REVERT: D 205 LYS cc_start: 0.9043 (ptpp) cc_final: 0.8719 (mtmm) REVERT: D 257 LYS cc_start: 0.9199 (ttmm) cc_final: 0.8826 (mttm) REVERT: D 323 VAL cc_start: 0.9794 (p) cc_final: 0.9465 (m) REVERT: D 408 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7671 (pp) REVERT: D 411 TYR cc_start: 0.9018 (t80) cc_final: 0.8666 (t80) REVERT: D 466 HIS cc_start: 0.7977 (t-90) cc_final: 0.7739 (t-90) REVERT: E 78 MET cc_start: 0.9227 (tpp) cc_final: 0.9010 (tpp) REVERT: E 129 ASP cc_start: 0.8330 (t0) cc_final: 0.8036 (t0) REVERT: E 153 LYS cc_start: 0.8334 (mtpp) cc_final: 0.8004 (mtpp) REVERT: E 286 MET cc_start: 0.8317 (tpp) cc_final: 0.7992 (tpp) REVERT: E 500 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7804 (mm-30) REVERT: F 75 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7398 (tt0) REVERT: F 286 MET cc_start: 0.8416 (tpp) cc_final: 0.8106 (tpp) REVERT: F 323 VAL cc_start: 0.9736 (p) cc_final: 0.9345 (m) REVERT: F 408 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7939 (pp) REVERT: F 466 HIS cc_start: 0.8183 (t-90) cc_final: 0.7948 (t-90) REVERT: G 103 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7937 (mm-30) REVERT: G 284 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8934 (tt) REVERT: H 32 TYR cc_start: 0.9203 (m-80) cc_final: 0.8421 (m-80) REVERT: H 78 MET cc_start: 0.9271 (tpp) cc_final: 0.9061 (tpp) REVERT: H 136 ARG cc_start: 0.7786 (ttm110) cc_final: 0.7552 (ttm110) REVERT: H 153 LYS cc_start: 0.8385 (mtpp) cc_final: 0.8129 (mtpp) REVERT: H 203 ARG cc_start: 0.7676 (ttp80) cc_final: 0.7275 (mtp-110) REVERT: H 286 MET cc_start: 0.8638 (tpt) cc_final: 0.8436 (tpp) REVERT: H 323 VAL cc_start: 0.9801 (p) cc_final: 0.9472 (m) REVERT: H 385 MET cc_start: 0.8780 (ttm) cc_final: 0.8390 (ttm) REVERT: H 411 TYR cc_start: 0.9075 (t80) cc_final: 0.8591 (t80) outliers start: 75 outliers final: 51 residues processed: 918 average time/residue: 0.7621 time to fit residues: 1144.3299 Evaluate side-chains 897 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 840 time to evaluate : 3.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 350 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 0.7980 chunk 334 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 371 optimal weight: 0.0870 chunk 308 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS C 466 HIS C 498 GLN F 498 GLN G 466 HIS ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 466 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 30840 Z= 0.208 Angle : 0.573 6.822 41952 Z= 0.290 Chirality : 0.043 0.152 4856 Planarity : 0.004 0.047 5160 Dihedral : 17.042 170.700 5135 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.17 % Allowed : 16.36 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 3800 helix: -0.03 (0.15), residues: 1272 sheet: -1.83 (0.20), residues: 544 loop : -0.93 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 466 PHE 0.011 0.001 PHE A 401 TYR 0.011 0.001 TYR E 400 ARG 0.003 0.000 ARG C 253 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 871 time to evaluate : 3.613 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: A 129 ASP cc_start: 0.8501 (t0) cc_final: 0.8268 (t0) REVERT: A 135 MET cc_start: 0.7929 (ttp) cc_final: 0.7720 (tmm) REVERT: A 179 MET cc_start: 0.8352 (pp-130) cc_final: 0.7942 (pp-130) REVERT: A 286 MET cc_start: 0.8664 (tpt) cc_final: 0.8457 (tpp) REVERT: B 286 MET cc_start: 0.8435 (tpp) cc_final: 0.8160 (tpp) REVERT: B 323 VAL cc_start: 0.9764 (p) cc_final: 0.9369 (m) REVERT: C 75 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7286 (tt0) REVERT: C 171 HIS cc_start: 0.7209 (m90) cc_final: 0.6695 (m90) REVERT: C 286 MET cc_start: 0.8633 (tpt) cc_final: 0.8165 (tpp) REVERT: C 408 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7606 (pp) REVERT: D 129 ASP cc_start: 0.8383 (t0) cc_final: 0.8078 (t0) REVERT: D 205 LYS cc_start: 0.9014 (ptpp) cc_final: 0.8704 (mtmm) REVERT: D 257 LYS cc_start: 0.9160 (ttmm) cc_final: 0.8822 (mttm) REVERT: D 323 VAL cc_start: 0.9789 (p) cc_final: 0.9463 (m) REVERT: D 408 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7624 (pp) REVERT: D 411 TYR cc_start: 0.9007 (t80) cc_final: 0.8667 (t80) REVERT: D 466 HIS cc_start: 0.7992 (t-90) cc_final: 0.7773 (t-90) REVERT: E 153 LYS cc_start: 0.8335 (mtpp) cc_final: 0.8005 (mtpp) REVERT: E 162 ASP cc_start: 0.8566 (m-30) cc_final: 0.8327 (m-30) REVERT: E 205 LYS cc_start: 0.9385 (ptpp) cc_final: 0.8831 (pttm) REVERT: E 286 MET cc_start: 0.8202 (tpp) cc_final: 0.7890 (tpp) REVERT: E 323 VAL cc_start: 0.9776 (p) cc_final: 0.9428 (m) REVERT: F 75 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7349 (tt0) REVERT: F 129 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7886 (t0) REVERT: F 286 MET cc_start: 0.8351 (tpp) cc_final: 0.8055 (tpp) REVERT: F 323 VAL cc_start: 0.9743 (p) cc_final: 0.9366 (m) REVERT: F 408 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7871 (pp) REVERT: G 103 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7778 (mm-30) REVERT: G 174 LEU cc_start: 0.8751 (tt) cc_final: 0.8397 (mp) REVERT: G 284 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8922 (tt) REVERT: G 500 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7530 (mm-30) REVERT: H 153 LYS cc_start: 0.8380 (mtpp) cc_final: 0.8118 (mtpp) REVERT: H 203 ARG cc_start: 0.7695 (ttp80) cc_final: 0.7263 (mtp-110) REVERT: H 323 VAL cc_start: 0.9796 (p) cc_final: 0.9464 (m) REVERT: H 408 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7694 (pp) REVERT: H 411 TYR cc_start: 0.9088 (t80) cc_final: 0.8693 (t80) outliers start: 68 outliers final: 48 residues processed: 910 average time/residue: 0.7279 time to fit residues: 1090.7418 Evaluate side-chains 907 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 851 time to evaluate : 3.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 408 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 271 optimal weight: 6.9990 chunk 210 optimal weight: 2.9990 chunk 312 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 370 optimal weight: 2.9990 chunk 231 optimal weight: 8.9990 chunk 225 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 30840 Z= 0.420 Angle : 0.646 7.142 41952 Z= 0.333 Chirality : 0.046 0.160 4856 Planarity : 0.005 0.054 5160 Dihedral : 17.409 168.431 5134 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 2.36 % Allowed : 16.96 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.13), residues: 3800 helix: -0.32 (0.14), residues: 1304 sheet: -2.06 (0.18), residues: 624 loop : -1.18 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS C 466 PHE 0.013 0.002 PHE F 35 TYR 0.012 0.001 TYR E 400 ARG 0.004 0.000 ARG F 493 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 874 time to evaluate : 3.527 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 135 MET cc_start: 0.7999 (ttp) cc_final: 0.7745 (tmm) REVERT: A 179 MET cc_start: 0.8386 (pp-130) cc_final: 0.7958 (pp-130) REVERT: A 408 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8386 (pp) REVERT: B 323 VAL cc_start: 0.9789 (p) cc_final: 0.9392 (m) REVERT: C 75 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7369 (tt0) REVERT: C 82 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8640 (ttm) REVERT: C 132 GLU cc_start: 0.7987 (tt0) cc_final: 0.7775 (tt0) REVERT: C 171 HIS cc_start: 0.7249 (m90) cc_final: 0.6628 (m90) REVERT: C 179 MET cc_start: 0.8972 (ppp) cc_final: 0.8460 (ppp) REVERT: C 286 MET cc_start: 0.8730 (tpt) cc_final: 0.8203 (tpp) REVERT: C 408 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7698 (pp) REVERT: D 32 TYR cc_start: 0.9209 (m-10) cc_final: 0.8362 (m-80) REVERT: D 129 ASP cc_start: 0.8523 (t0) cc_final: 0.8205 (t0) REVERT: D 205 LYS cc_start: 0.9008 (ptpp) cc_final: 0.8766 (mtmm) REVERT: D 257 LYS cc_start: 0.9194 (ttmm) cc_final: 0.8834 (mttm) REVERT: D 323 VAL cc_start: 0.9794 (p) cc_final: 0.9486 (m) REVERT: D 408 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7710 (pp) REVERT: D 466 HIS cc_start: 0.8220 (t-90) cc_final: 0.7995 (t-90) REVERT: E 153 LYS cc_start: 0.8303 (mtpp) cc_final: 0.7967 (mtpp) REVERT: E 205 LYS cc_start: 0.9409 (ptpp) cc_final: 0.8851 (pttm) REVERT: E 286 MET cc_start: 0.8364 (tpp) cc_final: 0.8014 (tpp) REVERT: E 335 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7619 (mm-30) REVERT: F 75 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7477 (tt0) REVERT: F 408 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7900 (pp) REVERT: G 103 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7959 (mm-30) REVERT: G 174 LEU cc_start: 0.8755 (tt) cc_final: 0.8465 (mp) REVERT: G 284 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.9055 (tt) REVERT: H 32 TYR cc_start: 0.9222 (m-80) cc_final: 0.8377 (m-80) REVERT: H 153 LYS cc_start: 0.8404 (mtpp) cc_final: 0.8102 (mtpp) REVERT: H 203 ARG cc_start: 0.7792 (ttp80) cc_final: 0.7381 (mtp-110) REVERT: H 286 MET cc_start: 0.8217 (tpp) cc_final: 0.7911 (tpp) REVERT: H 309 GLN cc_start: 0.9368 (OUTLIER) cc_final: 0.9032 (pt0) REVERT: H 323 VAL cc_start: 0.9805 (p) cc_final: 0.9485 (m) REVERT: H 385 MET cc_start: 0.8847 (ttm) cc_final: 0.8590 (ttm) REVERT: H 395 GLU cc_start: 0.8707 (mp0) cc_final: 0.8434 (mp0) REVERT: H 408 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7752 (pp) REVERT: H 411 TYR cc_start: 0.9064 (t80) cc_final: 0.8509 (t80) outliers start: 74 outliers final: 59 residues processed: 915 average time/residue: 0.7313 time to fit residues: 1096.3144 Evaluate side-chains 922 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 853 time to evaluate : 3.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 362 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 408 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 221 optimal weight: 0.0980 chunk 111 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 235 optimal weight: 1.9990 chunk 252 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 290 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN ** G 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 30840 Z= 0.210 Angle : 0.577 6.899 41952 Z= 0.293 Chirality : 0.043 0.152 4856 Planarity : 0.004 0.047 5160 Dihedral : 16.939 170.769 5134 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.39 % Allowed : 17.19 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.13), residues: 3800 helix: 0.01 (0.15), residues: 1272 sheet: -1.91 (0.20), residues: 544 loop : -0.90 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 466 PHE 0.012 0.001 PHE A 401 TYR 0.009 0.001 TYR E 400 ARG 0.003 0.000 ARG C 253 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 870 time to evaluate : 3.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.8472 (t0) cc_final: 0.8207 (t0) REVERT: A 179 MET cc_start: 0.8332 (pp-130) cc_final: 0.7918 (pp-130) REVERT: A 286 MET cc_start: 0.8681 (tpt) cc_final: 0.8240 (tpp) REVERT: A 408 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8420 (pp) REVERT: B 286 MET cc_start: 0.8367 (tpp) cc_final: 0.8125 (tpp) REVERT: B 323 VAL cc_start: 0.9776 (p) cc_final: 0.9380 (m) REVERT: C 75 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7291 (tt0) REVERT: C 82 MET cc_start: 0.9094 (ttm) cc_final: 0.8607 (ttm) REVERT: C 171 HIS cc_start: 0.7276 (m90) cc_final: 0.6642 (m90) REVERT: C 286 MET cc_start: 0.8673 (tpt) cc_final: 0.8210 (tpp) REVERT: C 408 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7611 (pp) REVERT: D 129 ASP cc_start: 0.8540 (t0) cc_final: 0.8225 (t0) REVERT: D 153 LYS cc_start: 0.8391 (mtpp) cc_final: 0.8168 (mtpp) REVERT: D 257 LYS cc_start: 0.9201 (ttmm) cc_final: 0.8866 (mttm) REVERT: D 323 VAL cc_start: 0.9797 (p) cc_final: 0.9493 (m) REVERT: D 408 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7660 (pp) REVERT: D 466 HIS cc_start: 0.8034 (t-90) cc_final: 0.7802 (t-90) REVERT: E 153 LYS cc_start: 0.8361 (mtpp) cc_final: 0.8058 (mtpp) REVERT: E 205 LYS cc_start: 0.9389 (ptpp) cc_final: 0.8847 (pttm) REVERT: E 323 VAL cc_start: 0.9792 (p) cc_final: 0.9447 (m) REVERT: F 75 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7369 (tt0) REVERT: F 323 VAL cc_start: 0.9753 (p) cc_final: 0.9363 (m) REVERT: F 408 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7871 (pp) REVERT: G 103 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7812 (mm-30) REVERT: G 174 LEU cc_start: 0.8769 (tt) cc_final: 0.8489 (mp) REVERT: H 103 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8201 (mm-30) REVERT: H 153 LYS cc_start: 0.8372 (mtpp) cc_final: 0.8081 (mtpp) REVERT: H 203 ARG cc_start: 0.7664 (ttp80) cc_final: 0.7266 (mtp180) REVERT: H 257 LYS cc_start: 0.9164 (ttmm) cc_final: 0.8910 (mttm) REVERT: H 286 MET cc_start: 0.8169 (tpp) cc_final: 0.7860 (tpp) REVERT: H 323 VAL cc_start: 0.9798 (p) cc_final: 0.9475 (m) REVERT: H 364 ASP cc_start: 0.8414 (t0) cc_final: 0.8196 (t0) REVERT: H 385 MET cc_start: 0.8837 (ttm) cc_final: 0.8234 (ttm) REVERT: H 395 GLU cc_start: 0.8686 (mp0) cc_final: 0.8465 (mp0) REVERT: H 408 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7706 (pp) REVERT: H 411 TYR cc_start: 0.9072 (t80) cc_final: 0.8632 (t80) outliers start: 75 outliers final: 59 residues processed: 912 average time/residue: 0.7189 time to fit residues: 1073.9268 Evaluate side-chains 924 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 858 time to evaluate : 3.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 408 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 0.7980 chunk 354 optimal weight: 4.9990 chunk 323 optimal weight: 2.9990 chunk 344 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 270 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 311 optimal weight: 2.9990 chunk 326 optimal weight: 0.9980 chunk 343 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN ** H 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 30840 Z= 0.234 Angle : 0.577 6.822 41952 Z= 0.293 Chirality : 0.043 0.152 4856 Planarity : 0.004 0.047 5160 Dihedral : 16.701 171.511 5134 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.46 % Allowed : 17.03 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.14), residues: 3800 helix: 0.07 (0.15), residues: 1240 sheet: -1.89 (0.20), residues: 544 loop : -0.83 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 466 PHE 0.012 0.001 PHE C 139 TYR 0.009 0.001 TYR E 400 ARG 0.003 0.000 ARG C 253 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 867 time to evaluate : 3.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.8472 (t0) cc_final: 0.8230 (t0) REVERT: A 179 MET cc_start: 0.8322 (pp-130) cc_final: 0.7915 (pp-130) REVERT: A 286 MET cc_start: 0.8680 (tpt) cc_final: 0.8242 (tpp) REVERT: A 408 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8426 (pp) REVERT: B 286 MET cc_start: 0.8356 (tpp) cc_final: 0.8128 (tpp) REVERT: B 323 VAL cc_start: 0.9777 (p) cc_final: 0.9378 (m) REVERT: C 75 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7245 (tt0) REVERT: C 82 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8685 (ttm) REVERT: C 171 HIS cc_start: 0.7306 (m90) cc_final: 0.6687 (m90) REVERT: C 286 MET cc_start: 0.8649 (tpt) cc_final: 0.8176 (tpp) REVERT: C 408 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7654 (pp) REVERT: D 129 ASP cc_start: 0.8538 (t0) cc_final: 0.8222 (t0) REVERT: D 153 LYS cc_start: 0.8395 (mtpp) cc_final: 0.8167 (mtpp) REVERT: D 206 LYS cc_start: 0.7871 (mttp) cc_final: 0.7652 (mtmp) REVERT: D 257 LYS cc_start: 0.9209 (ttmm) cc_final: 0.8847 (mttm) REVERT: D 323 VAL cc_start: 0.9791 (p) cc_final: 0.9489 (m) REVERT: D 408 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7622 (pp) REVERT: D 466 HIS cc_start: 0.8024 (t-90) cc_final: 0.7787 (t-90) REVERT: E 153 LYS cc_start: 0.8355 (mtpp) cc_final: 0.8045 (mtpp) REVERT: E 205 LYS cc_start: 0.9402 (ptpp) cc_final: 0.8957 (pttm) REVERT: E 206 LYS cc_start: 0.8108 (mttp) cc_final: 0.7756 (mttp) REVERT: E 323 VAL cc_start: 0.9787 (p) cc_final: 0.9429 (m) REVERT: F 75 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: F 323 VAL cc_start: 0.9755 (p) cc_final: 0.9360 (m) REVERT: F 408 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7891 (pp) REVERT: G 103 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7796 (mm-30) REVERT: G 174 LEU cc_start: 0.8777 (tt) cc_final: 0.8540 (mp) REVERT: H 103 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8175 (mm-30) REVERT: H 153 LYS cc_start: 0.8391 (mtpp) cc_final: 0.8076 (mtpp) REVERT: H 203 ARG cc_start: 0.7671 (ttp80) cc_final: 0.7255 (mtp180) REVERT: H 257 LYS cc_start: 0.9166 (ttmm) cc_final: 0.8914 (mttm) REVERT: H 286 MET cc_start: 0.8141 (tpp) cc_final: 0.7835 (tpp) REVERT: H 323 VAL cc_start: 0.9796 (p) cc_final: 0.9489 (m) REVERT: H 364 ASP cc_start: 0.8427 (t0) cc_final: 0.8142 (t0) REVERT: H 385 MET cc_start: 0.8842 (ttm) cc_final: 0.8184 (ttm) REVERT: H 395 GLU cc_start: 0.8695 (mp0) cc_final: 0.8454 (mp0) REVERT: H 408 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7724 (pp) REVERT: H 411 TYR cc_start: 0.9075 (t80) cc_final: 0.8598 (t80) REVERT: H 492 LYS cc_start: 0.8949 (mtmm) cc_final: 0.8747 (mtmt) outliers start: 77 outliers final: 63 residues processed: 911 average time/residue: 0.7444 time to fit residues: 1120.2830 Evaluate side-chains 938 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 867 time to evaluate : 3.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 362 ILE Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 408 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 0.9990 chunk 364 optimal weight: 0.5980 chunk 222 optimal weight: 1.9990 chunk 173 optimal weight: 0.5980 chunk 253 optimal weight: 1.9990 chunk 382 optimal weight: 0.8980 chunk 352 optimal weight: 0.9980 chunk 304 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 chunk 186 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30840 Z= 0.162 Angle : 0.555 6.710 41952 Z= 0.280 Chirality : 0.042 0.152 4856 Planarity : 0.004 0.046 5160 Dihedral : 16.258 173.446 5134 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.07 % Allowed : 17.35 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.14), residues: 3800 helix: 0.27 (0.15), residues: 1240 sheet: -1.64 (0.21), residues: 496 loop : -0.76 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS B 466 PHE 0.011 0.001 PHE A 401 TYR 0.008 0.001 TYR E 400 ARG 0.003 0.000 ARG C 253 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 926 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 861 time to evaluate : 3.587 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 129 ASP cc_start: 0.8443 (t0) cc_final: 0.8212 (t0) REVERT: A 179 MET cc_start: 0.8321 (pp-130) cc_final: 0.7914 (pp-130) REVERT: A 286 MET cc_start: 0.8657 (tpt) cc_final: 0.8248 (tpp) REVERT: A 408 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8437 (pp) REVERT: B 286 MET cc_start: 0.8313 (tpp) cc_final: 0.8085 (tpp) REVERT: B 323 VAL cc_start: 0.9785 (p) cc_final: 0.9399 (m) REVERT: C 82 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8763 (ttm) REVERT: C 171 HIS cc_start: 0.7305 (m90) cc_final: 0.6684 (m90) REVERT: C 254 GLU cc_start: 0.8817 (tp30) cc_final: 0.8573 (tm-30) REVERT: C 286 MET cc_start: 0.8639 (tpt) cc_final: 0.8427 (tpp) REVERT: C 408 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7625 (pp) REVERT: D 129 ASP cc_start: 0.8473 (t0) cc_final: 0.8152 (t0) REVERT: D 153 LYS cc_start: 0.8371 (mtpp) cc_final: 0.8155 (mtpp) REVERT: D 206 LYS cc_start: 0.7849 (mttp) cc_final: 0.7605 (mtmp) REVERT: D 257 LYS cc_start: 0.9203 (ttmm) cc_final: 0.8852 (mttm) REVERT: D 323 VAL cc_start: 0.9771 (p) cc_final: 0.9476 (m) REVERT: D 408 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7569 (pp) REVERT: E 153 LYS cc_start: 0.8353 (mtpp) cc_final: 0.8053 (mtpp) REVERT: E 205 LYS cc_start: 0.9372 (ptpp) cc_final: 0.8967 (pttm) REVERT: E 206 LYS cc_start: 0.8110 (mttp) cc_final: 0.7747 (mttp) REVERT: E 323 VAL cc_start: 0.9785 (p) cc_final: 0.9428 (m) REVERT: F 75 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7320 (tt0) REVERT: F 129 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7873 (t0) REVERT: F 286 MET cc_start: 0.8298 (tpp) cc_final: 0.8062 (tpp) REVERT: F 323 VAL cc_start: 0.9750 (p) cc_final: 0.9396 (m) REVERT: F 408 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7863 (pp) REVERT: G 103 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7702 (mm-30) REVERT: H 103 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8143 (mm-30) REVERT: H 153 LYS cc_start: 0.8378 (mtpp) cc_final: 0.8072 (mtpp) REVERT: H 203 ARG cc_start: 0.7617 (ttp80) cc_final: 0.7252 (mtp180) REVERT: H 257 LYS cc_start: 0.9147 (ttmm) cc_final: 0.8912 (mttm) REVERT: H 286 MET cc_start: 0.8067 (tpp) cc_final: 0.7765 (tpp) REVERT: H 323 VAL cc_start: 0.9762 (p) cc_final: 0.9442 (m) REVERT: H 364 ASP cc_start: 0.8373 (t0) cc_final: 0.8077 (t0) REVERT: H 385 MET cc_start: 0.8743 (ttm) cc_final: 0.8070 (ttm) REVERT: H 395 GLU cc_start: 0.8656 (mp0) cc_final: 0.8418 (mp0) REVERT: H 411 TYR cc_start: 0.9079 (t80) cc_final: 0.8535 (t80) REVERT: H 492 LYS cc_start: 0.8995 (mtmm) cc_final: 0.8784 (mtmt) outliers start: 65 outliers final: 52 residues processed: 901 average time/residue: 0.7442 time to fit residues: 1107.0415 Evaluate side-chains 910 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 851 time to evaluate : 3.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 362 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 2.9990 chunk 324 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 280 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 305 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 313 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 HIS ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.115066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.088270 restraints weight = 110837.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.093037 restraints weight = 53246.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.096265 restraints weight = 33249.864| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 30840 Z= 0.323 Angle : 0.602 6.790 41952 Z= 0.308 Chirality : 0.044 0.154 4856 Planarity : 0.004 0.047 5160 Dihedral : 16.514 172.507 5134 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.20 % Allowed : 17.54 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.14), residues: 3800 helix: 0.19 (0.15), residues: 1224 sheet: -2.04 (0.19), residues: 616 loop : -0.81 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS H 466 PHE 0.012 0.001 PHE C 139 TYR 0.010 0.001 TYR E 400 ARG 0.004 0.000 ARG E 253 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16086.71 seconds wall clock time: 277 minutes 0.75 seconds (16620.75 seconds total)