Starting phenix.real_space_refine on Thu Mar 5 14:45:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ua5_20706/03_2026/6ua5_20706.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ua5_20706/03_2026/6ua5_20706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ua5_20706/03_2026/6ua5_20706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ua5_20706/03_2026/6ua5_20706.map" model { file = "/net/cci-nas-00/data/ceres_data/6ua5_20706/03_2026/6ua5_20706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ua5_20706/03_2026/6ua5_20706.cif" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.102 sd= 3.978 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 144 5.16 5 C 14512 2.51 5 N 3920 2.21 5 O 4480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23080 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "B" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "C" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "D" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "E" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "F" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "G" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "H" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 5.21, per 1000 atoms: 0.23 Number of scatterers: 23080 At special positions: 0 Unit cell: (124.95, 124.95, 120.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 144 16.00 P 24 15.00 O 4480 8.00 N 3920 7.00 C 14512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 901.0 milliseconds 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5392 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 32 sheets defined 38.0% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 19 through 24 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 96 through 110 removed outlier: 3.603A pdb=" N LYS A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 256 through 267 removed outlier: 3.930A pdb=" N LEU A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 263 " --> pdb=" O ARG A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 291 removed outlier: 3.722A pdb=" N ILE A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 removed outlier: 4.216A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 343 through 356 removed outlier: 4.024A pdb=" N TYR A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 removed outlier: 3.549A pdb=" N ALA A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 455 Processing helix chain 'A' and resid 456 through 472 Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 502 removed outlier: 3.781A pdb=" N GLU A 500 " --> pdb=" O SER A 496 " (cutoff:3.500A) Processing helix 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 86 Processing helix chain 'B' and resid 96 through 110 removed outlier: 3.604A pdb=" N LYS B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 255 No H-bonds generated for 'chain 'B' and resid 253 through 255' Processing helix chain 'B' and resid 256 through 267 removed outlier: 3.930A pdb=" N LEU B 262 " --> pdb=" O TYR B 258 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 263 " --> pdb=" O ARG B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 291 removed outlier: 3.723A pdb=" N ILE B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 removed outlier: 4.216A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 343 through 356 removed outlier: 4.023A pdb=" N TYR B 348 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS B 349 " --> pdb=" O THR B 345 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 removed outlier: 3.551A pdb=" N ALA B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 455 Processing helix chain 'B' and resid 456 through 472 Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 502 removed outlier: 3.780A pdb=" N GLU B 500 " --> pdb=" O SER B 496 " (cutoff:3.500A) Processing helix 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 86 Processing helix chain 'C' and resid 96 through 110 removed outlier: 3.604A pdb=" N LYS C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR C 110 " --> pdb=" O LYS C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 256 through 267 removed outlier: 3.930A pdb=" N LEU C 262 " --> pdb=" O TYR C 258 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 263 " --> pdb=" O ARG C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 291 removed outlier: 3.723A pdb=" N ILE C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 removed outlier: 4.217A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 343 through 356 removed outlier: 4.025A pdb=" N TYR C 348 " --> pdb=" O ALA C 344 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS C 349 " --> pdb=" O THR C 345 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 378 removed outlier: 3.550A pdb=" N ALA C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 455 Processing helix chain 'C' and resid 456 through 472 Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 494 through 502 removed outlier: 3.780A pdb=" N GLU C 500 " --> pdb=" O SER C 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 75 through 86 Processing helix chain 'D' and resid 96 through 110 removed outlier: 3.604A pdb=" N LYS D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 256 through 267 removed outlier: 3.930A pdb=" N LEU D 262 " --> pdb=" O TYR D 258 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU D 263 " --> pdb=" O ARG D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 291 removed outlier: 3.723A pdb=" N ILE D 284 " --> pdb=" O SER D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 315 removed outlier: 4.217A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 343 through 356 removed outlier: 4.024A pdb=" N TYR D 348 " --> pdb=" O ALA D 344 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS D 349 " --> pdb=" O THR D 345 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 378 removed outlier: 3.550A pdb=" N ALA D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 455 Processing helix chain 'D' and resid 456 through 472 Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 502 removed outlier: 3.781A pdb=" N GLU D 500 " --> pdb=" O SER D 496 " (cutoff:3.500A) Processing helix 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 86 Processing helix chain 'E' and resid 96 through 110 removed outlier: 3.604A pdb=" N LYS E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR E 110 " --> pdb=" O LYS E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 255 No H-bonds generated for 'chain 'E' and resid 253 through 255' Processing helix chain 'E' and resid 256 through 267 removed outlier: 3.930A pdb=" N LEU E 262 " --> pdb=" O TYR E 258 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU E 263 " --> pdb=" O ARG E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 291 removed outlier: 3.722A pdb=" N ILE E 284 " --> pdb=" O SER E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 315 removed outlier: 4.217A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 343 through 356 removed outlier: 4.024A pdb=" N TYR E 348 " --> pdb=" O ALA E 344 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS E 349 " --> pdb=" O THR E 345 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 378 removed outlier: 3.550A pdb=" N ALA E 374 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 455 Processing helix chain 'E' and resid 456 through 472 Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 494 through 502 removed outlier: 3.781A pdb=" N GLU E 500 " --> pdb=" O SER E 496 " (cutoff:3.500A) Processing helix 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 86 Processing helix chain 'F' and resid 96 through 110 removed outlier: 3.604A pdb=" N LYS F 109 " --> pdb=" O ARG F 105 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 255 No H-bonds generated for 'chain 'F' and resid 253 through 255' Processing helix chain 'F' and resid 256 through 267 removed outlier: 3.929A pdb=" N LEU F 262 " --> pdb=" O TYR F 258 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU F 263 " --> pdb=" O ARG F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 291 removed outlier: 3.722A pdb=" N ILE F 284 " --> pdb=" O SER F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 315 removed outlier: 4.217A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 337 Processing helix chain 'F' and resid 343 through 356 removed outlier: 4.024A pdb=" N TYR F 348 " --> pdb=" O ALA F 344 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 378 removed outlier: 3.550A pdb=" N ALA F 374 " --> pdb=" O VAL F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 455 Processing helix chain 'F' and resid 456 through 472 Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 494 through 502 removed outlier: 3.781A pdb=" N GLU F 500 " --> pdb=" O SER F 496 " (cutoff:3.500A) Processing helix 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 86 Processing helix chain 'G' and resid 96 through 110 removed outlier: 3.604A pdb=" N LYS G 109 " --> pdb=" O ARG G 105 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR G 110 " --> pdb=" O LYS G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 255 No H-bonds generated for 'chain 'G' and resid 253 through 255' Processing helix chain 'G' and resid 256 through 267 removed outlier: 3.930A pdb=" N LEU G 262 " --> pdb=" O TYR G 258 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU G 263 " --> pdb=" O ARG G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 291 removed outlier: 3.723A pdb=" N ILE G 284 " --> pdb=" O SER G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 315 removed outlier: 4.217A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 337 Processing helix chain 'G' and resid 343 through 356 removed outlier: 4.024A pdb=" N TYR G 348 " --> pdb=" O ALA G 344 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS G 349 " --> pdb=" O THR G 345 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 378 removed outlier: 3.550A pdb=" N ALA G 374 " --> pdb=" O VAL G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 455 Processing helix chain 'G' and resid 456 through 472 Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'G' and resid 494 through 502 removed outlier: 3.781A pdb=" N GLU G 500 " --> pdb=" O SER G 496 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 24 Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 75 through 86 Processing helix chain 'H' and resid 96 through 110 removed outlier: 3.604A pdb=" N LYS H 109 " --> pdb=" O ARG H 105 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR H 110 " --> pdb=" O LYS H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 255 No H-bonds generated for 'chain 'H' and resid 253 through 255' Processing helix chain 'H' and resid 256 through 267 removed outlier: 3.930A pdb=" N LEU H 262 " --> pdb=" O TYR H 258 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU H 263 " --> pdb=" O ARG H 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 291 removed outlier: 3.723A pdb=" N ILE H 284 " --> pdb=" O SER H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 315 removed outlier: 4.217A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 337 Processing helix chain 'H' and resid 343 through 356 removed outlier: 4.024A pdb=" N TYR H 348 " --> pdb=" O ALA H 344 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS H 349 " --> pdb=" O THR H 345 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 378 removed outlier: 3.550A pdb=" N ALA H 374 " --> pdb=" O VAL H 370 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 455 Processing helix chain 'H' and resid 456 through 472 Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 494 through 502 removed outlier: 3.780A pdb=" N GLU H 500 " --> pdb=" O SER H 496 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.488A pdb=" N VAL A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N MET A 385 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 320 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 401 through 403 removed outlier: 3.980A pdb=" N SER A 444 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER D 508 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.887A pdb=" N SER A 508 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER B 444 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.488A pdb=" N VAL B 66 " --> pdb=" O MET B 386 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N MET B 385 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA B 320 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 508 through 510 removed outlier: 3.918A pdb=" N SER B 508 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER C 444 " --> pdb=" O GLU B 510 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.489A pdb=" N VAL C 66 " --> pdb=" O MET C 386 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N MET C 385 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA C 320 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASN C 303 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 508 through 510 removed outlier: 3.936A pdb=" N SER C 508 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER D 444 " --> pdb=" O GLU C 510 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.488A pdb=" N VAL D 66 " --> pdb=" O MET D 386 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N MET D 385 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA D 320 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AB9, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.487A pdb=" N VAL E 66 " --> pdb=" O MET E 386 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N MET E 385 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA E 320 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 401 through 403 removed outlier: 3.983A pdb=" N SER E 444 " --> pdb=" O GLU H 510 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER H 508 " --> pdb=" O ALA E 446 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 508 through 510 removed outlier: 4.020A pdb=" N SER E 508 " --> pdb=" O ALA F 446 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER F 444 " --> pdb=" O GLU E 510 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AC5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AC6, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.487A pdb=" N VAL F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N MET F 385 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA F 320 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 508 through 510 removed outlier: 3.953A pdb=" N SER F 508 " --> pdb=" O ALA G 446 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER G 444 " --> pdb=" O GLU F 510 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AC9, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AD1, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.488A pdb=" N VAL G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N MET G 385 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA G 320 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 508 through 510 removed outlier: 3.918A pdb=" N SER G 508 " --> pdb=" O ALA H 446 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER H 444 " --> pdb=" O GLU G 510 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AD4, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AD5, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.489A pdb=" N VAL H 66 " --> pdb=" O MET H 386 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N MET H 385 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA H 320 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASN H 303 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) 784 hydrogen bonds defined for protein. 2256 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: 3.94 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3848 1.30 - 1.43: 5812 1.43 - 1.56: 13468 1.56 - 1.68: 112 1.68 - 1.81: 240 Bond restraints: 23480 Sorted by residual: bond pdb=" C3D NAD D 602 " pdb=" C4D NAD D 602 " ideal model delta sigma weight residual 1.531 1.296 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C3D NAD E 602 " pdb=" C4D NAD E 602 " ideal model delta sigma weight residual 1.531 1.296 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C3D NAD A 602 " pdb=" C4D NAD A 602 " ideal model delta sigma weight residual 1.531 1.296 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C3D NAD G 602 " pdb=" C4D NAD G 602 " ideal model delta sigma weight residual 1.531 1.296 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C3D NAD C 602 " pdb=" C4D NAD C 602 " ideal model delta sigma weight residual 1.531 1.297 0.234 2.00e-02 2.50e+03 1.37e+02 ... (remaining 23475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 30373 3.21 - 6.42: 1155 6.42 - 9.63: 192 9.63 - 12.84: 48 12.84 - 16.05: 24 Bond angle restraints: 31792 Sorted by residual: angle pdb=" CB GLU C 103 " pdb=" CG GLU C 103 " pdb=" CD GLU C 103 " ideal model delta sigma weight residual 112.60 122.68 -10.08 1.70e+00 3.46e-01 3.52e+01 angle pdb=" CB GLU G 103 " pdb=" CG GLU G 103 " pdb=" CD GLU G 103 " ideal model delta sigma weight residual 112.60 122.67 -10.07 1.70e+00 3.46e-01 3.51e+01 angle pdb=" CB GLU D 103 " pdb=" CG GLU D 103 " pdb=" CD GLU D 103 " ideal model delta sigma weight residual 112.60 122.66 -10.06 1.70e+00 3.46e-01 3.50e+01 angle pdb=" CB GLU B 103 " pdb=" CG GLU B 103 " pdb=" CD GLU B 103 " ideal model delta sigma weight residual 112.60 122.65 -10.05 1.70e+00 3.46e-01 3.49e+01 angle pdb=" CB GLU E 103 " pdb=" CG GLU E 103 " pdb=" CD GLU E 103 " ideal model delta sigma weight residual 112.60 122.64 -10.04 1.70e+00 3.46e-01 3.49e+01 ... (remaining 31787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 12775 17.11 - 34.23: 945 34.23 - 51.34: 372 51.34 - 68.46: 136 68.46 - 85.57: 20 Dihedral angle restraints: 14248 sinusoidal: 5744 harmonic: 8504 Sorted by residual: dihedral pdb=" CA THR C 45 " pdb=" C THR C 45 " pdb=" N ALA C 46 " pdb=" CA ALA C 46 " ideal model delta harmonic sigma weight residual -180.00 -154.54 -25.46 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA THR H 45 " pdb=" C THR H 45 " pdb=" N ALA H 46 " pdb=" CA ALA H 46 " ideal model delta harmonic sigma weight residual 180.00 -154.61 -25.39 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA THR F 45 " pdb=" C THR F 45 " pdb=" N ALA F 46 " pdb=" CA ALA F 46 " ideal model delta harmonic sigma weight residual -180.00 -154.62 -25.38 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 14245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2516 0.067 - 0.134: 873 0.134 - 0.201: 218 0.201 - 0.268: 22 0.268 - 0.335: 27 Chirality restraints: 3656 Sorted by residual: chirality pdb=" CB VAL E 304 " pdb=" CA VAL E 304 " pdb=" CG1 VAL E 304 " pdb=" CG2 VAL E 304 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CB VAL D 304 " pdb=" CA VAL D 304 " pdb=" CG1 VAL D 304 " pdb=" CG2 VAL D 304 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CB VAL H 304 " pdb=" CA VAL H 304 " pdb=" CG1 VAL H 304 " pdb=" CG2 VAL H 304 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 3653 not shown) Planarity restraints: 4000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 63 " -0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO H 64 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO H 64 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 64 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 63 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO C 64 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 63 " -0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO E 64 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO E 64 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 64 " -0.032 5.00e-02 4.00e+02 ... (remaining 3997 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2957 2.73 - 3.28: 22133 3.28 - 3.82: 40140 3.82 - 4.36: 47474 4.36 - 4.90: 79366 Nonbonded interactions: 192070 Sorted by model distance: nonbonded pdb=" O GLY E 40 " pdb=" NE2 GLN F 277 " model vdw 2.192 3.120 nonbonded pdb=" O GLY F 40 " pdb=" NE2 GLN G 277 " model vdw 2.246 3.120 nonbonded pdb=" OG SER F 496 " pdb=" NE2 GLN G 498 " model vdw 2.250 3.120 nonbonded pdb=" OG SER E 496 " pdb=" NE2 GLN F 498 " model vdw 2.251 3.120 nonbonded pdb=" OG SER A 496 " pdb=" NE2 GLN B 498 " model vdw 2.263 3.120 ... (remaining 192065 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.200 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 : 0.014 0.235 23488 Z= 0.662 Angle : 1.502 16.046 31792 Z= 0.766 Chirality : 0.074 0.335 3656 Planarity : 0.007 0.058 4000 Dihedral : 15.754 85.571 8856 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 8.52 % Allowed : 9.94 % Favored : 81.54 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.43 (0.13), residues: 2960 helix: -3.82 (0.08), residues: 1120 sheet: -2.67 (0.24), residues: 400 loop : -2.13 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG G 355 TYR 0.031 0.003 TYR F 12 PHE 0.022 0.004 PHE A 401 HIS 0.012 0.002 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.01427 (23480) covalent geometry : angle 1.50189 (31792) hydrogen bonds : bond 0.18889 ( 784) hydrogen bonds : angle 7.95625 ( 2256) Misc. bond : bond 0.00325 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1123 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 920 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 HIS cc_start: 0.8632 (p90) cc_final: 0.8331 (p-80) REVERT: A 102 ASN cc_start: 0.8390 (t0) cc_final: 0.7733 (t0) REVERT: A 254 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7641 (tt0) REVERT: A 259 ARG cc_start: 0.8691 (ttm-80) cc_final: 0.8150 (ttm170) REVERT: A 274 ASP cc_start: 0.8673 (t0) cc_final: 0.8376 (t70) REVERT: A 315 ASP cc_start: 0.7280 (OUTLIER) cc_final: 0.7063 (m-30) REVERT: A 327 SER cc_start: 0.8695 (p) cc_final: 0.8159 (p) REVERT: A 359 VAL cc_start: 0.9365 (t) cc_final: 0.9010 (p) REVERT: A 386 MET cc_start: 0.8600 (mtm) cc_final: 0.8388 (mtm) REVERT: A 395 GLU cc_start: 0.8775 (mp0) cc_final: 0.8526 (mp0) REVERT: A 461 ILE cc_start: 0.9076 (pt) cc_final: 0.8617 (mt) REVERT: A 483 MET cc_start: 0.9226 (tmm) cc_final: 0.8744 (tmm) REVERT: B 32 TYR cc_start: 0.8655 (m-80) cc_final: 0.8426 (m-80) REVERT: B 92 HIS cc_start: 0.8702 (p90) cc_final: 0.8383 (p-80) REVERT: B 102 ASN cc_start: 0.8587 (t0) cc_final: 0.7938 (t0) REVERT: B 254 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7614 (tt0) REVERT: B 259 ARG cc_start: 0.8708 (ttm-80) cc_final: 0.8197 (ttm170) REVERT: B 274 ASP cc_start: 0.8723 (t0) cc_final: 0.8334 (t70) REVERT: B 315 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.7000 (m-30) REVERT: B 359 VAL cc_start: 0.9310 (t) cc_final: 0.8947 (p) REVERT: B 386 MET cc_start: 0.8626 (mtm) cc_final: 0.8410 (mtm) REVERT: B 483 MET cc_start: 0.9222 (tmm) cc_final: 0.8775 (tmm) REVERT: C 56 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8804 (p) REVERT: C 78 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7868 (ttp) REVERT: C 92 HIS cc_start: 0.8610 (p90) cc_final: 0.8249 (p-80) REVERT: C 102 ASN cc_start: 0.8547 (t0) cc_final: 0.7875 (t0) REVERT: C 254 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7758 (tt0) REVERT: C 274 ASP cc_start: 0.8709 (t0) cc_final: 0.8425 (t70) REVERT: C 296 ASN cc_start: 0.8687 (p0) cc_final: 0.8340 (p0) REVERT: C 327 SER cc_start: 0.8719 (p) cc_final: 0.8180 (p) REVERT: C 386 MET cc_start: 0.8684 (mtm) cc_final: 0.8446 (mtm) REVERT: C 395 GLU cc_start: 0.8760 (mp0) cc_final: 0.8547 (mp0) REVERT: C 483 MET cc_start: 0.9260 (tmm) cc_final: 0.8742 (tmm) REVERT: D 50 ASP cc_start: 0.8242 (t0) cc_final: 0.8023 (t0) REVERT: D 56 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8763 (p) REVERT: D 92 HIS cc_start: 0.8743 (p90) cc_final: 0.8379 (p-80) REVERT: D 102 ASN cc_start: 0.8692 (t0) cc_final: 0.8069 (t0) REVERT: D 254 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: D 274 ASP cc_start: 0.8733 (t0) cc_final: 0.8360 (t70) REVERT: D 283 GLN cc_start: 0.9027 (tt0) cc_final: 0.8811 (tt0) REVERT: D 296 ASN cc_start: 0.8668 (p0) cc_final: 0.8353 (p0) REVERT: D 386 MET cc_start: 0.8695 (mtm) cc_final: 0.8412 (mtm) REVERT: D 483 MET cc_start: 0.9227 (tmm) cc_final: 0.8778 (tmm) REVERT: E 78 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7759 (ttp) REVERT: E 92 HIS cc_start: 0.8470 (p90) cc_final: 0.8131 (p-80) REVERT: E 102 ASN cc_start: 0.8478 (t0) cc_final: 0.7799 (t0) REVERT: E 254 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7662 (tt0) REVERT: E 259 ARG cc_start: 0.8688 (ttm-80) cc_final: 0.8058 (ttm170) REVERT: E 315 ASP cc_start: 0.7125 (OUTLIER) cc_final: 0.6911 (m-30) REVERT: E 327 SER cc_start: 0.8865 (p) cc_final: 0.8383 (p) REVERT: E 386 MET cc_start: 0.8580 (mtm) cc_final: 0.8334 (mtm) REVERT: E 395 GLU cc_start: 0.8806 (mp0) cc_final: 0.8517 (mp0) REVERT: E 461 ILE cc_start: 0.9087 (pt) cc_final: 0.8616 (mt) REVERT: E 483 MET cc_start: 0.9248 (tmm) cc_final: 0.8733 (tmm) REVERT: E 510 GLU cc_start: 0.7023 (tm-30) cc_final: 0.6693 (tm-30) REVERT: F 92 HIS cc_start: 0.8576 (p90) cc_final: 0.8159 (p-80) REVERT: F 100 GLN cc_start: 0.9468 (OUTLIER) cc_final: 0.9246 (mt0) REVERT: F 102 ASN cc_start: 0.8792 (t0) cc_final: 0.8179 (t0) REVERT: F 254 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: F 285 ASN cc_start: 0.8842 (m110) cc_final: 0.8522 (m110) REVERT: F 315 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6910 (m-30) REVERT: F 327 SER cc_start: 0.8834 (p) cc_final: 0.8297 (p) REVERT: F 386 MET cc_start: 0.8736 (mtm) cc_final: 0.8478 (mtm) REVERT: F 483 MET cc_start: 0.9249 (tmm) cc_final: 0.8770 (tmm) REVERT: G 32 TYR cc_start: 0.8660 (m-80) cc_final: 0.8401 (m-80) REVERT: G 92 HIS cc_start: 0.8601 (p90) cc_final: 0.8314 (p-80) REVERT: G 102 ASN cc_start: 0.8473 (t0) cc_final: 0.7786 (t0) REVERT: G 254 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.7671 (tt0) REVERT: G 259 ARG cc_start: 0.8656 (ttm-80) cc_final: 0.8111 (ttm170) REVERT: G 274 ASP cc_start: 0.8719 (t0) cc_final: 0.8403 (t70) REVERT: G 296 ASN cc_start: 0.8747 (p0) cc_final: 0.8424 (p0) REVERT: G 315 ASP cc_start: 0.7334 (OUTLIER) cc_final: 0.7122 (m-30) REVERT: G 327 SER cc_start: 0.8800 (p) cc_final: 0.8276 (p) REVERT: G 359 VAL cc_start: 0.9359 (t) cc_final: 0.9023 (p) REVERT: G 386 MET cc_start: 0.8638 (mtm) cc_final: 0.8415 (mtm) REVERT: G 483 MET cc_start: 0.9208 (tmm) cc_final: 0.8766 (tmm) REVERT: H 92 HIS cc_start: 0.8766 (p90) cc_final: 0.8416 (p-80) REVERT: H 102 ASN cc_start: 0.8666 (t0) cc_final: 0.8018 (t0) REVERT: H 254 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7777 (tt0) REVERT: H 259 ARG cc_start: 0.8719 (ttm-80) cc_final: 0.8221 (ttm170) REVERT: H 274 ASP cc_start: 0.8757 (t0) cc_final: 0.8317 (t70) REVERT: H 296 ASN cc_start: 0.8623 (p0) cc_final: 0.8327 (p0) REVERT: H 315 ASP cc_start: 0.7278 (OUTLIER) cc_final: 0.7046 (m-30) REVERT: H 359 VAL cc_start: 0.9356 (t) cc_final: 0.8988 (p) REVERT: H 386 MET cc_start: 0.8692 (mtm) cc_final: 0.8415 (mtm) REVERT: H 483 MET cc_start: 0.9208 (tmm) cc_final: 0.8800 (tmm) outliers start: 203 outliers final: 93 residues processed: 991 average time/residue: 0.1525 time to fit residues: 237.7859 Evaluate side-chains 810 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 698 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 485 SER Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 485 SER Chi-restraints excluded: chain H residue 491 GLU Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.0970 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN A 303 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN A 498 GLN ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 303 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN B 498 GLN ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 GLN ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 GLN ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN D 298 GLN D 303 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN D 498 GLN ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN E 303 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 GLN F 100 GLN F 283 GLN F 303 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN F 465 GLN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 GLN G 303 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 GLN ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 GLN H 498 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.153481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.127118 restraints weight = 33406.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.132250 restraints weight = 17106.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.135721 restraints weight = 10725.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.138078 restraints weight = 7658.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.139731 restraints weight = 5977.546| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23488 Z= 0.147 Angle : 0.699 11.482 31792 Z= 0.358 Chirality : 0.046 0.173 3656 Planarity : 0.005 0.040 4000 Dihedral : 13.247 84.089 3944 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 5.16 % Allowed : 18.67 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.14), residues: 2960 helix: -2.32 (0.13), residues: 1000 sheet: -2.50 (0.25), residues: 384 loop : -1.16 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 412 TYR 0.017 0.002 TYR G 41 PHE 0.017 0.002 PHE H 44 HIS 0.005 0.001 HIS E 92 Details of bonding type rmsd covalent geometry : bond 0.00328 (23480) covalent geometry : angle 0.69887 (31792) hydrogen bonds : bond 0.03329 ( 784) hydrogen bonds : angle 5.73947 ( 2256) Misc. bond : bond 0.00022 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 805 time to evaluate : 0.807 Fit side-chains REVERT: A 43 ASP cc_start: 0.7666 (m-30) cc_final: 0.7460 (m-30) REVERT: A 102 ASN cc_start: 0.8436 (t0) cc_final: 0.7753 (t0) REVERT: A 274 ASP cc_start: 0.8842 (t0) cc_final: 0.8566 (t70) REVERT: A 296 ASN cc_start: 0.8429 (p0) cc_final: 0.8129 (p0) REVERT: A 327 SER cc_start: 0.8698 (p) cc_final: 0.8252 (p) REVERT: A 461 ILE cc_start: 0.8812 (pt) cc_final: 0.8609 (mt) REVERT: A 491 GLU cc_start: 0.8352 (tp30) cc_final: 0.8135 (tp30) REVERT: B 102 ASN cc_start: 0.8595 (t0) cc_final: 0.7960 (t0) REVERT: B 241 LYS cc_start: 0.9106 (tppt) cc_final: 0.8842 (tppt) REVERT: B 274 ASP cc_start: 0.8873 (t0) cc_final: 0.8502 (t70) REVERT: B 289 TYR cc_start: 0.9080 (t80) cc_final: 0.8870 (t80) REVERT: B 461 ILE cc_start: 0.8939 (pt) cc_final: 0.8574 (mt) REVERT: B 483 MET cc_start: 0.9118 (tmm) cc_final: 0.8652 (tmm) REVERT: C 56 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8487 (p) REVERT: C 102 ASN cc_start: 0.8504 (t0) cc_final: 0.7733 (t0) REVERT: C 103 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8058 (tp30) REVERT: C 274 ASP cc_start: 0.8769 (t0) cc_final: 0.8525 (t70) REVERT: C 296 ASN cc_start: 0.8513 (p0) cc_final: 0.8226 (p0) REVERT: C 327 SER cc_start: 0.8658 (p) cc_final: 0.8229 (p) REVERT: C 461 ILE cc_start: 0.9005 (pt) cc_final: 0.8593 (mt) REVERT: C 491 GLU cc_start: 0.8529 (tp30) cc_final: 0.8322 (tp30) REVERT: D 56 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8444 (p) REVERT: D 102 ASN cc_start: 0.8673 (t0) cc_final: 0.7953 (t0) REVERT: D 103 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8265 (tp30) REVERT: D 274 ASP cc_start: 0.8880 (t0) cc_final: 0.8525 (t70) REVERT: D 296 ASN cc_start: 0.8594 (p0) cc_final: 0.8259 (p0) REVERT: D 395 GLU cc_start: 0.8668 (mp0) cc_final: 0.8401 (mp0) REVERT: D 409 LYS cc_start: 0.8472 (ptpt) cc_final: 0.8267 (ptpt) REVERT: D 461 ILE cc_start: 0.8938 (pt) cc_final: 0.8519 (mt) REVERT: D 483 MET cc_start: 0.9167 (tmm) cc_final: 0.8633 (tmm) REVERT: E 42 ILE cc_start: 0.8169 (pt) cc_final: 0.7893 (pt) REVERT: E 43 ASP cc_start: 0.7775 (m-30) cc_final: 0.7556 (m-30) REVERT: E 102 ASN cc_start: 0.8431 (t0) cc_final: 0.7846 (t0) REVERT: E 259 ARG cc_start: 0.8553 (ttm-80) cc_final: 0.8226 (tpp80) REVERT: E 269 ASP cc_start: 0.8695 (m-30) cc_final: 0.8444 (m-30) REVERT: E 296 ASN cc_start: 0.8577 (p0) cc_final: 0.8207 (p0) REVERT: E 327 SER cc_start: 0.8762 (p) cc_final: 0.8309 (p) REVERT: E 399 GLU cc_start: 0.8085 (pm20) cc_final: 0.7779 (pp20) REVERT: E 483 MET cc_start: 0.9205 (tmm) cc_final: 0.8573 (tmm) REVERT: F 82 MET cc_start: 0.8712 (mtp) cc_final: 0.8441 (mtp) REVERT: F 102 ASN cc_start: 0.8718 (t0) cc_final: 0.8067 (t0) REVERT: F 259 ARG cc_start: 0.8561 (ttm-80) cc_final: 0.8114 (tpp80) REVERT: F 285 ASN cc_start: 0.8823 (m110) cc_final: 0.8576 (m110) REVERT: F 296 ASN cc_start: 0.8694 (p0) cc_final: 0.8281 (p0) REVERT: F 319 ASP cc_start: 0.8091 (t0) cc_final: 0.7873 (t0) REVERT: F 327 SER cc_start: 0.8741 (p) cc_final: 0.8337 (p) REVERT: F 461 ILE cc_start: 0.8952 (pt) cc_final: 0.8570 (mt) REVERT: F 483 MET cc_start: 0.9167 (tmm) cc_final: 0.8628 (tmm) REVERT: G 102 ASN cc_start: 0.8405 (t0) cc_final: 0.7668 (t0) REVERT: G 259 ARG cc_start: 0.8619 (ttm-80) cc_final: 0.8113 (ttm110) REVERT: G 274 ASP cc_start: 0.8868 (t0) cc_final: 0.8609 (t70) REVERT: G 296 ASN cc_start: 0.8578 (p0) cc_final: 0.8272 (p0) REVERT: G 327 SER cc_start: 0.8749 (p) cc_final: 0.8260 (p) REVERT: G 395 GLU cc_start: 0.8619 (mp0) cc_final: 0.8262 (mp0) REVERT: G 461 ILE cc_start: 0.8907 (pt) cc_final: 0.8465 (mt) REVERT: G 483 MET cc_start: 0.9121 (tmm) cc_final: 0.8611 (tmm) REVERT: G 491 GLU cc_start: 0.8369 (tp30) cc_final: 0.8136 (tp30) REVERT: H 102 ASN cc_start: 0.8630 (t0) cc_final: 0.7957 (t0) REVERT: H 241 LYS cc_start: 0.9187 (tppt) cc_final: 0.8966 (tppt) REVERT: H 258 TYR cc_start: 0.8687 (t80) cc_final: 0.8438 (t80) REVERT: H 274 ASP cc_start: 0.8819 (t0) cc_final: 0.8235 (t70) REVERT: H 296 ASN cc_start: 0.8542 (p0) cc_final: 0.8213 (p0) REVERT: H 395 GLU cc_start: 0.8710 (mp0) cc_final: 0.8301 (mp0) REVERT: H 409 LYS cc_start: 0.8402 (ptpt) cc_final: 0.8186 (ptpt) REVERT: H 461 ILE cc_start: 0.8873 (pt) cc_final: 0.8427 (mt) REVERT: H 483 MET cc_start: 0.9129 (tmm) cc_final: 0.8590 (tmm) outliers start: 123 outliers final: 55 residues processed: 855 average time/residue: 0.1488 time to fit residues: 202.3759 Evaluate side-chains 764 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 705 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 498 GLN Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 146 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 262 optimal weight: 0.0970 chunk 8 optimal weight: 0.7980 chunk 248 optimal weight: 0.9980 chunk 179 optimal weight: 5.9990 chunk 122 optimal weight: 0.0040 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 GLN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 ASN ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.155267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.128781 restraints weight = 33104.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.133976 restraints weight = 17014.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.137438 restraints weight = 10681.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.139790 restraints weight = 7642.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.141440 restraints weight = 5989.701| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23488 Z= 0.133 Angle : 0.684 18.054 31792 Z= 0.333 Chirality : 0.046 0.148 3656 Planarity : 0.004 0.032 4000 Dihedral : 10.959 88.338 3794 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.89 % Allowed : 24.41 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.15), residues: 2960 helix: -1.52 (0.14), residues: 1040 sheet: -2.36 (0.23), residues: 432 loop : -0.99 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 355 TYR 0.026 0.002 TYR G 289 PHE 0.016 0.002 PHE H 44 HIS 0.008 0.001 HIS F 92 Details of bonding type rmsd covalent geometry : bond 0.00314 (23480) covalent geometry : angle 0.68375 (31792) hydrogen bonds : bond 0.03235 ( 784) hydrogen bonds : angle 5.23726 ( 2256) Misc. bond : bond 0.00025 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 764 time to evaluate : 0.836 Fit side-chains REVERT: A 43 ASP cc_start: 0.7786 (m-30) cc_final: 0.7494 (m-30) REVERT: A 102 ASN cc_start: 0.8501 (t0) cc_final: 0.7794 (t0) REVERT: A 259 ARG cc_start: 0.8919 (tpp80) cc_final: 0.8568 (tpp80) REVERT: A 274 ASP cc_start: 0.8705 (t0) cc_final: 0.8273 (t70) REVERT: A 441 GLN cc_start: 0.8623 (mt0) cc_final: 0.8330 (mt0) REVERT: A 461 ILE cc_start: 0.8772 (pt) cc_final: 0.8537 (mt) REVERT: A 483 MET cc_start: 0.9114 (tmm) cc_final: 0.8617 (tmm) REVERT: B 75 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7255 (mm-30) REVERT: B 102 ASN cc_start: 0.8680 (t0) cc_final: 0.8001 (t0) REVERT: B 259 ARG cc_start: 0.8795 (ttm-80) cc_final: 0.8461 (tpp80) REVERT: B 274 ASP cc_start: 0.8741 (t0) cc_final: 0.8170 (t70) REVERT: B 399 GLU cc_start: 0.8095 (pm20) cc_final: 0.7894 (mp0) REVERT: B 461 ILE cc_start: 0.8889 (pt) cc_final: 0.8549 (mt) REVERT: B 483 MET cc_start: 0.9153 (tmm) cc_final: 0.8671 (tmm) REVERT: B 491 GLU cc_start: 0.8404 (tp30) cc_final: 0.8186 (tp30) REVERT: C 102 ASN cc_start: 0.8631 (t0) cc_final: 0.7882 (t0) REVERT: C 259 ARG cc_start: 0.8860 (tpp80) cc_final: 0.8566 (tpp80) REVERT: C 274 ASP cc_start: 0.8755 (t0) cc_final: 0.8313 (t70) REVERT: C 461 ILE cc_start: 0.8886 (pt) cc_final: 0.8576 (mt) REVERT: C 483 MET cc_start: 0.9136 (tmm) cc_final: 0.8602 (tmm) REVERT: D 56 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8418 (p) REVERT: D 59 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7744 (pt) REVERT: D 102 ASN cc_start: 0.8744 (t0) cc_final: 0.8073 (t0) REVERT: D 259 ARG cc_start: 0.8911 (tpp80) cc_final: 0.8341 (tpp80) REVERT: D 274 ASP cc_start: 0.8804 (t0) cc_final: 0.8290 (t70) REVERT: D 461 ILE cc_start: 0.8904 (pt) cc_final: 0.8548 (mt) REVERT: D 483 MET cc_start: 0.9151 (tmm) cc_final: 0.8572 (tmm) REVERT: E 42 ILE cc_start: 0.8326 (pt) cc_final: 0.7923 (pt) REVERT: E 43 ASP cc_start: 0.7859 (m-30) cc_final: 0.7570 (m-30) REVERT: E 102 ASN cc_start: 0.8567 (t0) cc_final: 0.7802 (t0) REVERT: E 296 ASN cc_start: 0.8517 (p0) cc_final: 0.8187 (p0) REVERT: E 327 SER cc_start: 0.8504 (p) cc_final: 0.8172 (p) REVERT: E 441 GLN cc_start: 0.8571 (mt0) cc_final: 0.8272 (mt0) REVERT: E 453 ILE cc_start: 0.9037 (pp) cc_final: 0.8792 (pt) REVERT: E 483 MET cc_start: 0.9169 (tmm) cc_final: 0.8682 (tmm) REVERT: E 491 GLU cc_start: 0.8487 (tp30) cc_final: 0.8276 (tp30) REVERT: F 78 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7761 (ttp) REVERT: F 102 ASN cc_start: 0.8865 (t0) cc_final: 0.8167 (t0) REVERT: F 245 LEU cc_start: 0.8866 (mt) cc_final: 0.8664 (mt) REVERT: F 259 ARG cc_start: 0.8634 (ttm-80) cc_final: 0.8081 (tpp80) REVERT: F 285 ASN cc_start: 0.8889 (m110) cc_final: 0.8637 (m110) REVERT: F 296 ASN cc_start: 0.8626 (p0) cc_final: 0.8234 (p0) REVERT: F 461 ILE cc_start: 0.8925 (pt) cc_final: 0.8600 (mt) REVERT: G 102 ASN cc_start: 0.8512 (t0) cc_final: 0.7741 (t0) REVERT: G 259 ARG cc_start: 0.8519 (ttm-80) cc_final: 0.8181 (tpp80) REVERT: G 274 ASP cc_start: 0.8789 (t0) cc_final: 0.8364 (t70) REVERT: G 327 SER cc_start: 0.8465 (p) cc_final: 0.8097 (p) REVERT: G 441 GLN cc_start: 0.8598 (mt0) cc_final: 0.8315 (mt0) REVERT: G 461 ILE cc_start: 0.8868 (pt) cc_final: 0.8536 (mt) REVERT: G 483 MET cc_start: 0.9212 (tmm) cc_final: 0.8752 (tmm) REVERT: H 102 ASN cc_start: 0.8730 (t0) cc_final: 0.8088 (t0) REVERT: H 242 LYS cc_start: 0.8269 (mttp) cc_final: 0.7936 (tppt) REVERT: H 259 ARG cc_start: 0.8864 (tpp80) cc_final: 0.8361 (tpp80) REVERT: H 274 ASP cc_start: 0.8821 (t0) cc_final: 0.8081 (t70) REVERT: H 409 LYS cc_start: 0.8285 (ptpt) cc_final: 0.8062 (ptpt) REVERT: H 461 ILE cc_start: 0.8860 (pt) cc_final: 0.8489 (mt) REVERT: H 483 MET cc_start: 0.9106 (tmm) cc_final: 0.8552 (tmm) outliers start: 69 outliers final: 40 residues processed: 792 average time/residue: 0.1496 time to fit residues: 186.8257 Evaluate side-chains 722 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 679 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 312 ASN Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 505 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 290 optimal weight: 0.8980 chunk 275 optimal weight: 4.9990 chunk 225 optimal weight: 0.6980 chunk 145 optimal weight: 0.0980 chunk 21 optimal weight: 5.9990 chunk 280 optimal weight: 0.7980 chunk 219 optimal weight: 2.9990 chunk 229 optimal weight: 6.9990 chunk 228 optimal weight: 0.3980 chunk 214 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 GLN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 GLN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 GLN ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.154020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.127589 restraints weight = 33115.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.132586 restraints weight = 17175.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.136114 restraints weight = 10882.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.138534 restraints weight = 7782.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.140095 restraints weight = 6055.671| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23488 Z= 0.127 Angle : 0.644 10.168 31792 Z= 0.319 Chirality : 0.045 0.280 3656 Planarity : 0.004 0.062 4000 Dihedral : 9.927 89.943 3761 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.90 % Allowed : 27.27 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.15), residues: 2960 helix: -0.98 (0.15), residues: 1016 sheet: -2.40 (0.22), residues: 432 loop : -0.86 (0.17), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 355 TYR 0.026 0.002 TYR B 289 PHE 0.012 0.001 PHE E 401 HIS 0.009 0.001 HIS F 92 Details of bonding type rmsd covalent geometry : bond 0.00298 (23480) covalent geometry : angle 0.64436 (31792) hydrogen bonds : bond 0.02971 ( 784) hydrogen bonds : angle 5.01290 ( 2256) Misc. bond : bond 0.00020 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 753 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: A 43 ASP cc_start: 0.7796 (m-30) cc_final: 0.7499 (m-30) REVERT: A 75 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7201 (mm-30) REVERT: A 102 ASN cc_start: 0.8616 (t0) cc_final: 0.7893 (t0) REVERT: A 259 ARG cc_start: 0.8841 (tpp80) cc_final: 0.8321 (tpp80) REVERT: A 274 ASP cc_start: 0.8702 (t0) cc_final: 0.8271 (t70) REVERT: A 399 GLU cc_start: 0.7728 (mp0) cc_final: 0.7484 (mp0) REVERT: A 441 GLN cc_start: 0.8603 (mt0) cc_final: 0.8332 (mt0) REVERT: A 461 ILE cc_start: 0.8742 (pt) cc_final: 0.8539 (mt) REVERT: A 483 MET cc_start: 0.9152 (tmm) cc_final: 0.8652 (tmm) REVERT: B 92 HIS cc_start: 0.8518 (p-80) cc_final: 0.8312 (p90) REVERT: B 102 ASN cc_start: 0.8715 (t0) cc_final: 0.8051 (t0) REVERT: B 242 LYS cc_start: 0.8271 (mttp) cc_final: 0.7942 (tppt) REVERT: B 259 ARG cc_start: 0.8733 (ttm-80) cc_final: 0.8416 (tpp80) REVERT: B 274 ASP cc_start: 0.8696 (t0) cc_final: 0.8108 (t70) REVERT: B 399 GLU cc_start: 0.7992 (pm20) cc_final: 0.7768 (mp0) REVERT: B 461 ILE cc_start: 0.8895 (pt) cc_final: 0.8619 (mt) REVERT: B 483 MET cc_start: 0.9162 (tmm) cc_final: 0.8657 (tmm) REVERT: B 491 GLU cc_start: 0.8459 (tp30) cc_final: 0.8134 (tp30) REVERT: C 102 ASN cc_start: 0.8730 (t0) cc_final: 0.7964 (t0) REVERT: C 254 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7537 (tt0) REVERT: C 258 TYR cc_start: 0.8481 (t80) cc_final: 0.8267 (t80) REVERT: C 259 ARG cc_start: 0.8856 (tpp80) cc_final: 0.8568 (tpp80) REVERT: C 274 ASP cc_start: 0.8730 (t0) cc_final: 0.8305 (t70) REVERT: C 399 GLU cc_start: 0.7730 (mp0) cc_final: 0.7502 (mp0) REVERT: C 453 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8473 (pt) REVERT: C 461 ILE cc_start: 0.8904 (pt) cc_final: 0.8642 (mt) REVERT: C 483 MET cc_start: 0.9174 (tmm) cc_final: 0.8639 (tmm) REVERT: D 56 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8242 (p) REVERT: D 59 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7755 (pt) REVERT: D 92 HIS cc_start: 0.8289 (p-80) cc_final: 0.8082 (p90) REVERT: D 102 ASN cc_start: 0.8845 (t0) cc_final: 0.8168 (t0) REVERT: D 259 ARG cc_start: 0.8879 (tpp80) cc_final: 0.8344 (tpp80) REVERT: D 274 ASP cc_start: 0.8744 (t0) cc_final: 0.8202 (t70) REVERT: D 461 ILE cc_start: 0.8810 (pt) cc_final: 0.8486 (mt) REVERT: D 483 MET cc_start: 0.9162 (tmm) cc_final: 0.8607 (tmm) REVERT: E 12 TYR cc_start: 0.8062 (t80) cc_final: 0.7843 (t80) REVERT: E 42 ILE cc_start: 0.8390 (pt) cc_final: 0.7964 (pt) REVERT: E 43 ASP cc_start: 0.7897 (m-30) cc_final: 0.7622 (m-30) REVERT: E 102 ASN cc_start: 0.8610 (t0) cc_final: 0.7840 (t0) REVERT: E 259 ARG cc_start: 0.8895 (tpp80) cc_final: 0.8693 (tpp80) REVERT: E 296 ASN cc_start: 0.8463 (p0) cc_final: 0.8170 (p0) REVERT: E 441 GLN cc_start: 0.8611 (mt0) cc_final: 0.8322 (mt0) REVERT: E 453 ILE cc_start: 0.9131 (pp) cc_final: 0.8880 (pt) REVERT: E 483 MET cc_start: 0.9194 (tmm) cc_final: 0.8658 (tmm) REVERT: E 491 GLU cc_start: 0.8541 (tp30) cc_final: 0.8234 (tp30) REVERT: F 78 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7593 (ttp) REVERT: F 102 ASN cc_start: 0.8848 (t0) cc_final: 0.8158 (t0) REVERT: F 245 LEU cc_start: 0.8799 (mt) cc_final: 0.8534 (mt) REVERT: F 259 ARG cc_start: 0.8636 (ttm-80) cc_final: 0.8066 (tpp80) REVERT: F 285 ASN cc_start: 0.8919 (m110) cc_final: 0.8656 (m110) REVERT: F 296 ASN cc_start: 0.8608 (p0) cc_final: 0.8236 (p0) REVERT: F 461 ILE cc_start: 0.8874 (pt) cc_final: 0.8569 (mt) REVERT: G 102 ASN cc_start: 0.8557 (t0) cc_final: 0.7807 (t0) REVERT: G 259 ARG cc_start: 0.8540 (ttm-80) cc_final: 0.8262 (tpp80) REVERT: G 274 ASP cc_start: 0.8778 (t0) cc_final: 0.8281 (t70) REVERT: G 399 GLU cc_start: 0.7712 (mp0) cc_final: 0.7487 (mp0) REVERT: G 441 GLN cc_start: 0.8588 (mt0) cc_final: 0.8321 (mt0) REVERT: G 448 GLN cc_start: 0.7665 (pt0) cc_final: 0.7443 (pt0) REVERT: G 461 ILE cc_start: 0.8836 (pt) cc_final: 0.8505 (mt) REVERT: H 92 HIS cc_start: 0.8440 (p-80) cc_final: 0.8236 (p90) REVERT: H 102 ASN cc_start: 0.8931 (t0) cc_final: 0.8418 (t0) REVERT: H 242 LYS cc_start: 0.8256 (mttp) cc_final: 0.7916 (tppt) REVERT: H 259 ARG cc_start: 0.8849 (tpp80) cc_final: 0.8399 (tpp80) REVERT: H 274 ASP cc_start: 0.8779 (t0) cc_final: 0.8286 (t70) REVERT: H 409 LYS cc_start: 0.8321 (ptpt) cc_final: 0.8039 (ptpt) REVERT: H 461 ILE cc_start: 0.8796 (pt) cc_final: 0.8478 (mt) REVERT: H 483 MET cc_start: 0.9180 (tmm) cc_final: 0.8730 (tmm) outliers start: 93 outliers final: 50 residues processed: 807 average time/residue: 0.1516 time to fit residues: 193.5008 Evaluate side-chains 736 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 681 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 505 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 282 optimal weight: 5.9990 chunk 142 optimal weight: 0.6980 chunk 177 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN A 243 GLN A 253 HIS ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN B 253 HIS ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN C 253 HIS C 283 GLN ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN D 253 HIS D 309 GLN D 312 ASN ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN F 253 HIS F 283 GLN F 309 GLN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 253 HIS ** G 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN H 100 GLN H 253 HIS H 283 GLN ** H 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.133042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.108508 restraints weight = 33424.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.112814 restraints weight = 18038.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.115824 restraints weight = 11623.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.117921 restraints weight = 8436.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.119400 restraints weight = 6652.486| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 23488 Z= 0.391 Angle : 0.877 8.918 31792 Z= 0.446 Chirality : 0.054 0.223 3656 Planarity : 0.006 0.100 4000 Dihedral : 10.736 89.986 3757 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 6.12 % Allowed : 26.89 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.15), residues: 2960 helix: -1.18 (0.14), residues: 1088 sheet: -2.58 (0.29), residues: 280 loop : -1.19 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 355 TYR 0.037 0.003 TYR B 12 PHE 0.016 0.002 PHE F 401 HIS 0.011 0.002 HIS F 92 Details of bonding type rmsd covalent geometry : bond 0.00907 (23480) covalent geometry : angle 0.87673 (31792) hydrogen bonds : bond 0.03734 ( 784) hydrogen bonds : angle 5.38140 ( 2256) Misc. bond : bond 0.00349 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 688 time to evaluate : 0.954 Fit side-chains REVERT: A 42 ILE cc_start: 0.8767 (pt) cc_final: 0.8431 (pt) REVERT: A 43 ASP cc_start: 0.8217 (m-30) cc_final: 0.8007 (m-30) REVERT: A 102 ASN cc_start: 0.8588 (t0) cc_final: 0.7876 (t0) REVERT: A 241 LYS cc_start: 0.9264 (tppt) cc_final: 0.9006 (tppt) REVERT: A 259 ARG cc_start: 0.8917 (tpp80) cc_final: 0.8571 (tpp80) REVERT: A 274 ASP cc_start: 0.9071 (t0) cc_final: 0.8798 (t70) REVERT: A 395 GLU cc_start: 0.8537 (mp0) cc_final: 0.8337 (mp0) REVERT: A 441 GLN cc_start: 0.8759 (mt0) cc_final: 0.8469 (mt0) REVERT: A 461 ILE cc_start: 0.8747 (pt) cc_final: 0.8514 (mt) REVERT: A 483 MET cc_start: 0.9163 (tmm) cc_final: 0.8717 (tmm) REVERT: B 92 HIS cc_start: 0.8769 (p-80) cc_final: 0.8466 (p90) REVERT: B 102 ASN cc_start: 0.8760 (t0) cc_final: 0.8118 (t0) REVERT: B 242 LYS cc_start: 0.8445 (mttp) cc_final: 0.8158 (tppt) REVERT: B 259 ARG cc_start: 0.8920 (ttm-80) cc_final: 0.8541 (tpp80) REVERT: B 274 ASP cc_start: 0.9129 (t0) cc_final: 0.8778 (t70) REVERT: B 395 GLU cc_start: 0.8556 (mp0) cc_final: 0.8286 (mp0) REVERT: B 441 GLN cc_start: 0.8754 (mt0) cc_final: 0.8388 (mt0) REVERT: B 461 ILE cc_start: 0.8907 (pt) cc_final: 0.8519 (mt) REVERT: B 483 MET cc_start: 0.9193 (tmm) cc_final: 0.8813 (tmm) REVERT: B 491 GLU cc_start: 0.8606 (tp30) cc_final: 0.8323 (tp30) REVERT: B 513 LEU cc_start: 0.8701 (mt) cc_final: 0.8483 (mt) REVERT: C 71 ASP cc_start: 0.8918 (p0) cc_final: 0.8618 (p0) REVERT: C 82 MET cc_start: 0.8623 (mtm) cc_final: 0.8178 (mtp) REVERT: C 102 ASN cc_start: 0.8638 (t0) cc_final: 0.7887 (t0) REVERT: C 259 ARG cc_start: 0.8985 (tpp80) cc_final: 0.8654 (tpp80) REVERT: C 274 ASP cc_start: 0.9036 (t0) cc_final: 0.8792 (t70) REVERT: C 395 GLU cc_start: 0.8538 (mp0) cc_final: 0.8324 (mp0) REVERT: C 441 GLN cc_start: 0.8766 (mt0) cc_final: 0.8406 (mt0) REVERT: C 461 ILE cc_start: 0.8939 (pt) cc_final: 0.8603 (mt) REVERT: C 483 MET cc_start: 0.9223 (tmm) cc_final: 0.8791 (tmm) REVERT: C 513 LEU cc_start: 0.8601 (mt) cc_final: 0.8380 (mt) REVERT: D 92 HIS cc_start: 0.8759 (p-80) cc_final: 0.8516 (p90) REVERT: D 102 ASN cc_start: 0.8924 (t0) cc_final: 0.8396 (t0) REVERT: D 259 ARG cc_start: 0.8982 (tpp80) cc_final: 0.8602 (tpp80) REVERT: D 274 ASP cc_start: 0.9099 (t0) cc_final: 0.8737 (t70) REVERT: D 483 MET cc_start: 0.9212 (tmm) cc_final: 0.8794 (tmm) REVERT: E 71 ASP cc_start: 0.8900 (p0) cc_final: 0.8582 (p0) REVERT: E 102 ASN cc_start: 0.8610 (t0) cc_final: 0.7871 (t0) REVERT: E 385 MET cc_start: 0.8841 (ttm) cc_final: 0.8574 (ttm) REVERT: E 395 GLU cc_start: 0.8526 (mp0) cc_final: 0.8151 (mp0) REVERT: E 441 GLN cc_start: 0.8763 (mt0) cc_final: 0.8438 (mt0) REVERT: E 483 MET cc_start: 0.9190 (tmm) cc_final: 0.8818 (tmm) REVERT: E 491 GLU cc_start: 0.8749 (tp30) cc_final: 0.8545 (tp30) REVERT: F 78 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7774 (ttp) REVERT: F 102 ASN cc_start: 0.8874 (t0) cc_final: 0.8239 (t0) REVERT: F 259 ARG cc_start: 0.8892 (ttm-80) cc_final: 0.8421 (tpp80) REVERT: F 296 ASN cc_start: 0.8604 (p0) cc_final: 0.8244 (p0) REVERT: F 487 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7919 (mm-30) REVERT: G 71 ASP cc_start: 0.8965 (p0) cc_final: 0.8656 (p0) REVERT: G 102 ASN cc_start: 0.8586 (t0) cc_final: 0.7867 (t0) REVERT: G 259 ARG cc_start: 0.8873 (ttm-80) cc_final: 0.8540 (tpp80) REVERT: G 274 ASP cc_start: 0.9089 (t0) cc_final: 0.8826 (t70) REVERT: G 385 MET cc_start: 0.8905 (ttm) cc_final: 0.8680 (ttm) REVERT: G 441 GLN cc_start: 0.8736 (mt0) cc_final: 0.8460 (mt0) REVERT: G 461 ILE cc_start: 0.8790 (pt) cc_final: 0.8429 (mt) REVERT: H 4 TYR cc_start: 0.8770 (t80) cc_final: 0.8570 (t80) REVERT: H 65 LEU cc_start: 0.9556 (mm) cc_final: 0.9339 (mm) REVERT: H 92 HIS cc_start: 0.8691 (p-80) cc_final: 0.8420 (p90) REVERT: H 102 ASN cc_start: 0.8985 (t0) cc_final: 0.8486 (t0) REVERT: H 242 LYS cc_start: 0.8455 (mttp) cc_final: 0.8144 (tppt) REVERT: H 259 ARG cc_start: 0.9002 (tpp80) cc_final: 0.8648 (tpp80) REVERT: H 274 ASP cc_start: 0.9127 (t0) cc_final: 0.8595 (t70) REVERT: H 483 MET cc_start: 0.9170 (tmm) cc_final: 0.8823 (tmm) REVERT: H 513 LEU cc_start: 0.8591 (mt) cc_final: 0.8388 (mt) outliers start: 146 outliers final: 91 residues processed: 800 average time/residue: 0.1427 time to fit residues: 181.8367 Evaluate side-chains 749 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 657 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 498 GLN Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 388 SER Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain H residue 498 GLN Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 505 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 147 optimal weight: 0.9980 chunk 175 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 223 optimal weight: 8.9990 chunk 189 optimal weight: 0.9990 chunk 269 optimal weight: 0.6980 chunk 242 optimal weight: 2.9990 chunk 277 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 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 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN B 368 GLN C 283 GLN ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.144302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.119315 restraints weight = 32938.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.124097 restraints weight = 17320.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.127285 restraints weight = 10939.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.129535 restraints weight = 7861.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.131115 restraints weight = 6139.389| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23488 Z= 0.152 Angle : 0.673 9.313 31792 Z= 0.342 Chirality : 0.047 0.218 3656 Planarity : 0.004 0.048 4000 Dihedral : 9.808 89.501 3756 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.61 % Allowed : 29.57 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.16), residues: 2960 helix: -0.43 (0.16), residues: 1024 sheet: -3.23 (0.29), residues: 256 loop : -0.83 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 480 TYR 0.027 0.002 TYR C 12 PHE 0.015 0.001 PHE F 99 HIS 0.009 0.001 HIS F 92 Details of bonding type rmsd covalent geometry : bond 0.00359 (23480) covalent geometry : angle 0.67337 (31792) hydrogen bonds : bond 0.02975 ( 784) hydrogen bonds : angle 5.04842 ( 2256) Misc. bond : bond 0.00045 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 682 time to evaluate : 0.850 Fit side-chains REVERT: A 43 ASP cc_start: 0.8028 (m-30) cc_final: 0.7713 (m-30) REVERT: A 102 ASN cc_start: 0.8661 (t0) cc_final: 0.7926 (t0) REVERT: A 259 ARG cc_start: 0.8865 (tpp80) cc_final: 0.8563 (tpp80) REVERT: A 274 ASP cc_start: 0.8914 (t0) cc_final: 0.8518 (t70) REVERT: A 441 GLN cc_start: 0.8687 (mt0) cc_final: 0.8360 (mt0) REVERT: A 483 MET cc_start: 0.9167 (tmm) cc_final: 0.8634 (tmm) REVERT: B 82 MET cc_start: 0.8421 (mtp) cc_final: 0.8119 (mtm) REVERT: B 92 HIS cc_start: 0.8666 (p-80) cc_final: 0.8287 (p90) REVERT: B 102 ASN cc_start: 0.8813 (t0) cc_final: 0.8136 (t0) REVERT: B 242 LYS cc_start: 0.8421 (mttp) cc_final: 0.8091 (tppt) REVERT: B 259 ARG cc_start: 0.8829 (ttm-80) cc_final: 0.8318 (tpp80) REVERT: B 274 ASP cc_start: 0.8924 (t0) cc_final: 0.8404 (t70) REVERT: B 441 GLN cc_start: 0.8665 (mt0) cc_final: 0.8267 (mt0) REVERT: B 461 ILE cc_start: 0.8829 (pt) cc_final: 0.8454 (mt) REVERT: B 483 MET cc_start: 0.9200 (tmm) cc_final: 0.8698 (tmm) REVERT: B 491 GLU cc_start: 0.8708 (tp30) cc_final: 0.8406 (tp30) REVERT: C 67 SER cc_start: 0.8562 (OUTLIER) cc_final: 0.8144 (p) REVERT: C 71 ASP cc_start: 0.8755 (p0) cc_final: 0.8437 (p0) REVERT: C 78 MET cc_start: 0.8584 (tpp) cc_final: 0.7959 (tpt) REVERT: C 102 ASN cc_start: 0.8724 (t0) cc_final: 0.7973 (t0) REVERT: C 259 ARG cc_start: 0.8892 (tpp80) cc_final: 0.8335 (tpp80) REVERT: C 274 ASP cc_start: 0.9004 (t0) cc_final: 0.8589 (t70) REVERT: C 441 GLN cc_start: 0.8700 (mt0) cc_final: 0.8299 (mt0) REVERT: C 461 ILE cc_start: 0.8863 (pt) cc_final: 0.8506 (mt) REVERT: C 483 MET cc_start: 0.9201 (tmm) cc_final: 0.8648 (tmm) REVERT: C 491 GLU cc_start: 0.8734 (tp30) cc_final: 0.8327 (tp30) REVERT: D 82 MET cc_start: 0.8708 (mtp) cc_final: 0.8492 (mtm) REVERT: D 92 HIS cc_start: 0.8631 (p-80) cc_final: 0.8360 (p90) REVERT: D 102 ASN cc_start: 0.8937 (t0) cc_final: 0.8395 (t0) REVERT: D 259 ARG cc_start: 0.8912 (tpp80) cc_final: 0.8369 (tpp80) REVERT: D 274 ASP cc_start: 0.8961 (t0) cc_final: 0.8415 (t70) REVERT: D 399 GLU cc_start: 0.7982 (mp0) cc_final: 0.7639 (mp0) REVERT: D 461 ILE cc_start: 0.8898 (pt) cc_final: 0.8426 (mt) REVERT: D 483 MET cc_start: 0.9211 (tmm) cc_final: 0.8678 (tmm) REVERT: E 78 MET cc_start: 0.8492 (tpp) cc_final: 0.8045 (tpp) REVERT: E 102 ASN cc_start: 0.8663 (t0) cc_final: 0.7932 (t0) REVERT: E 395 GLU cc_start: 0.8561 (mp0) cc_final: 0.8228 (mp0) REVERT: E 441 GLN cc_start: 0.8694 (mt0) cc_final: 0.8379 (mt0) REVERT: E 483 MET cc_start: 0.9208 (tmm) cc_final: 0.8719 (tmm) REVERT: E 491 GLU cc_start: 0.8733 (tp30) cc_final: 0.8497 (tp30) REVERT: F 102 ASN cc_start: 0.8869 (t0) cc_final: 0.8226 (t0) REVERT: F 395 GLU cc_start: 0.8846 (mp0) cc_final: 0.8552 (mp0) REVERT: F 441 GLN cc_start: 0.8643 (mt0) cc_final: 0.8306 (mt0) REVERT: F 461 ILE cc_start: 0.8912 (pt) cc_final: 0.8414 (mt) REVERT: G 102 ASN cc_start: 0.8666 (t0) cc_final: 0.7912 (t0) REVERT: G 274 ASP cc_start: 0.8994 (t0) cc_final: 0.8601 (t70) REVERT: G 286 MET cc_start: 0.8915 (mmm) cc_final: 0.8629 (tpp) REVERT: G 385 MET cc_start: 0.8830 (ttm) cc_final: 0.8496 (ttm) REVERT: G 441 GLN cc_start: 0.8689 (mt0) cc_final: 0.8383 (mt0) REVERT: G 461 ILE cc_start: 0.8736 (pt) cc_final: 0.8224 (mt) REVERT: G 483 MET cc_start: 0.9077 (tmm) cc_final: 0.8668 (tmm) REVERT: H 92 HIS cc_start: 0.8607 (p-80) cc_final: 0.8340 (p90) REVERT: H 102 ASN cc_start: 0.9026 (t0) cc_final: 0.8599 (t0) REVERT: H 242 LYS cc_start: 0.8382 (mttp) cc_final: 0.8113 (tppt) REVERT: H 259 ARG cc_start: 0.8898 (tpp80) cc_final: 0.8413 (tpp80) REVERT: H 274 ASP cc_start: 0.8930 (t0) cc_final: 0.8192 (t70) REVERT: H 355 ARG cc_start: 0.8785 (ttp-170) cc_final: 0.8347 (ttp-170) REVERT: H 461 ILE cc_start: 0.8844 (pt) cc_final: 0.8383 (mt) REVERT: H 483 MET cc_start: 0.9207 (tmm) cc_final: 0.8747 (tmm) REVERT: H 487 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7827 (mm-30) outliers start: 110 outliers final: 71 residues processed: 763 average time/residue: 0.1460 time to fit residues: 176.5223 Evaluate side-chains 724 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 652 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 505 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 207 optimal weight: 0.9990 chunk 233 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 80 optimal weight: 0.1980 chunk 115 optimal weight: 7.9990 chunk 295 optimal weight: 0.8980 chunk 281 optimal weight: 0.7980 chunk 252 optimal weight: 0.0670 chunk 133 optimal weight: 0.7980 chunk 103 optimal weight: 0.1980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.152127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.125636 restraints weight = 33543.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.130715 restraints weight = 17405.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.134258 restraints weight = 10993.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.136582 restraints weight = 7829.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.138360 restraints weight = 6120.344| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23488 Z= 0.126 Angle : 0.656 9.603 31792 Z= 0.329 Chirality : 0.045 0.207 3656 Planarity : 0.004 0.061 4000 Dihedral : 9.084 89.937 3753 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.28 % Allowed : 30.49 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.15), residues: 2960 helix: -0.08 (0.16), residues: 1016 sheet: -3.17 (0.28), residues: 256 loop : -0.86 (0.16), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 356 TYR 0.031 0.002 TYR C 12 PHE 0.016 0.001 PHE G 357 HIS 0.009 0.001 HIS F 92 Details of bonding type rmsd covalent geometry : bond 0.00292 (23480) covalent geometry : angle 0.65643 (31792) hydrogen bonds : bond 0.02828 ( 784) hydrogen bonds : angle 4.88119 ( 2256) Misc. bond : bond 0.00024 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 730 time to evaluate : 0.848 Fit side-chains REVERT: A 5 LEU cc_start: 0.8977 (pt) cc_final: 0.8747 (pt) REVERT: A 43 ASP cc_start: 0.7899 (m-30) cc_final: 0.7565 (m-30) REVERT: A 102 ASN cc_start: 0.8728 (t0) cc_final: 0.8015 (t0) REVERT: A 259 ARG cc_start: 0.8891 (tpp80) cc_final: 0.8570 (tpp80) REVERT: A 274 ASP cc_start: 0.8797 (t0) cc_final: 0.8314 (t70) REVERT: A 286 MET cc_start: 0.8935 (mmm) cc_final: 0.8513 (tpp) REVERT: A 386 MET cc_start: 0.9262 (ptp) cc_final: 0.8842 (pmm) REVERT: A 441 GLN cc_start: 0.8677 (mt0) cc_final: 0.8368 (mt0) REVERT: A 465 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8548 (mm-40) REVERT: A 483 MET cc_start: 0.9180 (tmm) cc_final: 0.8737 (tmm) REVERT: A 491 GLU cc_start: 0.8655 (tp30) cc_final: 0.8428 (tp30) REVERT: B 82 MET cc_start: 0.8556 (mtp) cc_final: 0.8215 (mtm) REVERT: B 92 HIS cc_start: 0.8665 (p-80) cc_final: 0.8259 (p90) REVERT: B 102 ASN cc_start: 0.8852 (t0) cc_final: 0.8211 (t0) REVERT: B 242 LYS cc_start: 0.8430 (mttp) cc_final: 0.8070 (tppt) REVERT: B 259 ARG cc_start: 0.8789 (ttm-80) cc_final: 0.8341 (tpp80) REVERT: B 274 ASP cc_start: 0.8810 (t0) cc_final: 0.8433 (t70) REVERT: B 399 GLU cc_start: 0.7892 (mp0) cc_final: 0.7577 (mp0) REVERT: B 441 GLN cc_start: 0.8636 (mt0) cc_final: 0.8346 (mt0) REVERT: B 461 ILE cc_start: 0.8878 (pt) cc_final: 0.8527 (mt) REVERT: B 483 MET cc_start: 0.9174 (tmm) cc_final: 0.8712 (tmm) REVERT: B 491 GLU cc_start: 0.8706 (tp30) cc_final: 0.8392 (tp30) REVERT: C 67 SER cc_start: 0.8656 (OUTLIER) cc_final: 0.8128 (p) REVERT: C 68 SER cc_start: 0.9235 (p) cc_final: 0.8785 (p) REVERT: C 102 ASN cc_start: 0.8736 (t0) cc_final: 0.8046 (t0) REVERT: C 258 TYR cc_start: 0.8585 (t80) cc_final: 0.8364 (t80) REVERT: C 259 ARG cc_start: 0.8854 (tpp80) cc_final: 0.8320 (tpp80) REVERT: C 274 ASP cc_start: 0.8803 (t0) cc_final: 0.8289 (t70) REVERT: C 441 GLN cc_start: 0.8645 (mt0) cc_final: 0.8332 (mt0) REVERT: C 465 GLN cc_start: 0.8821 (mt0) cc_final: 0.8582 (mm-40) REVERT: C 483 MET cc_start: 0.9193 (tmm) cc_final: 0.8693 (tmm) REVERT: D 92 HIS cc_start: 0.8519 (p-80) cc_final: 0.8296 (p90) REVERT: D 102 ASN cc_start: 0.8938 (t0) cc_final: 0.8398 (t0) REVERT: D 259 ARG cc_start: 0.8874 (tpp80) cc_final: 0.8307 (tpp80) REVERT: D 274 ASP cc_start: 0.8847 (t0) cc_final: 0.8227 (t70) REVERT: D 355 ARG cc_start: 0.8744 (ttp-170) cc_final: 0.8527 (ttp-170) REVERT: D 399 GLU cc_start: 0.7893 (mp0) cc_final: 0.7607 (mp0) REVERT: D 483 MET cc_start: 0.9187 (tmm) cc_final: 0.8718 (tmm) REVERT: E 43 ASP cc_start: 0.7982 (m-30) cc_final: 0.7723 (m-30) REVERT: E 68 SER cc_start: 0.9163 (p) cc_final: 0.8939 (p) REVERT: E 78 MET cc_start: 0.8509 (tpp) cc_final: 0.8187 (tpp) REVERT: E 102 ASN cc_start: 0.8702 (t0) cc_final: 0.7990 (t0) REVERT: E 441 GLN cc_start: 0.8715 (mt0) cc_final: 0.8469 (mt0) REVERT: E 483 MET cc_start: 0.9201 (tmm) cc_final: 0.8782 (tmm) REVERT: E 491 GLU cc_start: 0.8750 (tp30) cc_final: 0.8526 (tp30) REVERT: F 102 ASN cc_start: 0.8913 (t0) cc_final: 0.8331 (t0) REVERT: F 409 LYS cc_start: 0.8285 (ptpt) cc_final: 0.8034 (ptpt) REVERT: F 441 GLN cc_start: 0.8647 (mt0) cc_final: 0.8347 (mt0) REVERT: F 461 ILE cc_start: 0.8939 (pt) cc_final: 0.8438 (mt) REVERT: F 483 MET cc_start: 0.9082 (tmm) cc_final: 0.8680 (ttp) REVERT: G 102 ASN cc_start: 0.8705 (t0) cc_final: 0.7967 (t0) REVERT: G 274 ASP cc_start: 0.8869 (t0) cc_final: 0.8436 (t70) REVERT: G 441 GLN cc_start: 0.8702 (mt0) cc_final: 0.8462 (mt0) REVERT: G 491 GLU cc_start: 0.8647 (tp30) cc_final: 0.8410 (tp30) REVERT: H 92 HIS cc_start: 0.8591 (p-80) cc_final: 0.8298 (p90) REVERT: H 102 ASN cc_start: 0.9035 (t0) cc_final: 0.8628 (t0) REVERT: H 242 LYS cc_start: 0.8371 (mttp) cc_final: 0.8018 (tppt) REVERT: H 259 ARG cc_start: 0.8834 (tpp80) cc_final: 0.8365 (tpp80) REVERT: H 274 ASP cc_start: 0.8841 (t0) cc_final: 0.8338 (t70) REVERT: H 441 GLN cc_start: 0.8709 (mt0) cc_final: 0.8422 (mt0) REVERT: H 461 ILE cc_start: 0.8803 (pt) cc_final: 0.8273 (mt) REVERT: H 465 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8378 (mm-40) REVERT: H 483 MET cc_start: 0.9182 (tmm) cc_final: 0.8753 (tmm) outliers start: 102 outliers final: 60 residues processed: 797 average time/residue: 0.1494 time to fit residues: 188.7308 Evaluate side-chains 743 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 680 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 465 GLN Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 505 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 180 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 227 optimal weight: 0.4980 chunk 225 optimal weight: 0.3980 chunk 287 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 247 optimal weight: 0.9980 chunk 292 optimal weight: 0.7980 chunk 185 optimal weight: 3.9990 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 243 GLN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 GLN C 368 GLN E 100 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 GLN ** G 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.151270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.125159 restraints weight = 33376.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.130121 restraints weight = 17366.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.133469 restraints weight = 10988.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.135905 restraints weight = 7878.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.137507 restraints weight = 6150.815| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23488 Z= 0.137 Angle : 0.673 12.091 31792 Z= 0.336 Chirality : 0.045 0.200 3656 Planarity : 0.004 0.062 4000 Dihedral : 8.794 88.794 3748 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.36 % Allowed : 30.79 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.15), residues: 2960 helix: 0.07 (0.16), residues: 1016 sheet: -2.53 (0.28), residues: 304 loop : -0.82 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 356 TYR 0.035 0.002 TYR H 12 PHE 0.013 0.001 PHE H 44 HIS 0.010 0.001 HIS F 92 Details of bonding type rmsd covalent geometry : bond 0.00326 (23480) covalent geometry : angle 0.67286 (31792) hydrogen bonds : bond 0.02861 ( 784) hydrogen bonds : angle 4.78923 ( 2256) Misc. bond : bond 0.00050 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 718 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 5 LEU cc_start: 0.9094 (pt) cc_final: 0.8755 (pt) REVERT: A 43 ASP cc_start: 0.7747 (m-30) cc_final: 0.7421 (m-30) REVERT: A 51 LEU cc_start: 0.9215 (tp) cc_final: 0.8785 (tt) REVERT: A 78 MET cc_start: 0.8372 (tpp) cc_final: 0.8054 (tpp) REVERT: A 102 ASN cc_start: 0.8811 (t0) cc_final: 0.8135 (t0) REVERT: A 259 ARG cc_start: 0.8881 (tpp80) cc_final: 0.8552 (tpp80) REVERT: A 274 ASP cc_start: 0.8784 (t0) cc_final: 0.8349 (t70) REVERT: A 286 MET cc_start: 0.8787 (mmm) cc_final: 0.8478 (tpp) REVERT: A 386 MET cc_start: 0.9300 (ptp) cc_final: 0.8716 (pmm) REVERT: A 441 GLN cc_start: 0.8683 (mt0) cc_final: 0.8380 (mt0) REVERT: A 465 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8566 (mm-40) REVERT: A 483 MET cc_start: 0.9179 (tmm) cc_final: 0.8718 (tmm) REVERT: A 491 GLU cc_start: 0.8676 (tp30) cc_final: 0.8374 (tp30) REVERT: B 5 LEU cc_start: 0.9077 (pt) cc_final: 0.8742 (pt) REVERT: B 92 HIS cc_start: 0.8680 (p-80) cc_final: 0.8278 (p90) REVERT: B 102 ASN cc_start: 0.8877 (t0) cc_final: 0.8229 (t0) REVERT: B 242 LYS cc_start: 0.8462 (mttp) cc_final: 0.8067 (tppt) REVERT: B 259 ARG cc_start: 0.8788 (ttm-80) cc_final: 0.8330 (tpp80) REVERT: B 274 ASP cc_start: 0.8807 (t0) cc_final: 0.8176 (t70) REVERT: B 441 GLN cc_start: 0.8666 (mt0) cc_final: 0.8360 (mt0) REVERT: B 461 ILE cc_start: 0.8886 (pt) cc_final: 0.8523 (mt) REVERT: B 491 GLU cc_start: 0.8732 (tp30) cc_final: 0.8414 (tp30) REVERT: C 50 ASP cc_start: 0.8418 (t0) cc_final: 0.8186 (t0) REVERT: C 68 SER cc_start: 0.9274 (p) cc_final: 0.8963 (p) REVERT: C 78 MET cc_start: 0.8138 (tpp) cc_final: 0.7809 (tpp) REVERT: C 102 ASN cc_start: 0.8716 (t0) cc_final: 0.7999 (t0) REVERT: C 258 TYR cc_start: 0.8556 (t80) cc_final: 0.8328 (t80) REVERT: C 259 ARG cc_start: 0.8753 (tpp80) cc_final: 0.8232 (tpp80) REVERT: C 274 ASP cc_start: 0.8829 (t0) cc_final: 0.8353 (t70) REVERT: C 441 GLN cc_start: 0.8675 (mt0) cc_final: 0.8343 (mt0) REVERT: C 483 MET cc_start: 0.9194 (tmm) cc_final: 0.8762 (tmm) REVERT: D 59 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7796 (pt) REVERT: D 92 HIS cc_start: 0.8601 (p-80) cc_final: 0.8316 (p90) REVERT: D 102 ASN cc_start: 0.8982 (t0) cc_final: 0.8446 (t0) REVERT: D 103 GLU cc_start: 0.9065 (tp30) cc_final: 0.8809 (tp30) REVERT: D 259 ARG cc_start: 0.8875 (tpp80) cc_final: 0.8499 (tpp80) REVERT: D 274 ASP cc_start: 0.8845 (t0) cc_final: 0.8250 (t70) REVERT: D 399 GLU cc_start: 0.7874 (mp0) cc_final: 0.7608 (mp0) REVERT: D 448 GLN cc_start: 0.7675 (pt0) cc_final: 0.7471 (pt0) REVERT: D 483 MET cc_start: 0.9194 (tmm) cc_final: 0.8754 (tmm) REVERT: E 43 ASP cc_start: 0.7979 (m-30) cc_final: 0.7711 (m-30) REVERT: E 78 MET cc_start: 0.8442 (tpp) cc_final: 0.8155 (tpp) REVERT: E 102 ASN cc_start: 0.8719 (t0) cc_final: 0.8017 (t0) REVERT: E 441 GLN cc_start: 0.8724 (mt0) cc_final: 0.8433 (mt0) REVERT: E 483 MET cc_start: 0.9205 (tmm) cc_final: 0.8823 (tmm) REVERT: E 491 GLU cc_start: 0.8739 (tp30) cc_final: 0.8522 (tp30) REVERT: F 102 ASN cc_start: 0.8907 (t0) cc_final: 0.8327 (t0) REVERT: F 441 GLN cc_start: 0.8659 (mt0) cc_final: 0.8350 (mt0) REVERT: F 461 ILE cc_start: 0.8937 (pt) cc_final: 0.8439 (mt) REVERT: G 102 ASN cc_start: 0.8760 (t0) cc_final: 0.8058 (t0) REVERT: G 274 ASP cc_start: 0.8896 (t0) cc_final: 0.8445 (t70) REVERT: G 312 ASN cc_start: 0.9221 (m-40) cc_final: 0.8631 (m-40) REVERT: G 441 GLN cc_start: 0.8699 (mt0) cc_final: 0.8453 (mt0) REVERT: G 483 MET cc_start: 0.9102 (tmm) cc_final: 0.8742 (tmm) REVERT: H 5 LEU cc_start: 0.8695 (pt) cc_final: 0.8325 (pt) REVERT: H 92 HIS cc_start: 0.8631 (p-80) cc_final: 0.8311 (p90) REVERT: H 102 ASN cc_start: 0.9041 (t0) cc_final: 0.8579 (t0) REVERT: H 242 LYS cc_start: 0.8383 (mttp) cc_final: 0.8007 (tppt) REVERT: H 259 ARG cc_start: 0.8824 (tpp80) cc_final: 0.8354 (tpp80) REVERT: H 274 ASP cc_start: 0.8857 (t0) cc_final: 0.8371 (t70) REVERT: H 286 MET cc_start: 0.8952 (mmm) cc_final: 0.8606 (tpp) REVERT: H 441 GLN cc_start: 0.8693 (mt0) cc_final: 0.8395 (mt0) REVERT: H 461 ILE cc_start: 0.8831 (pt) cc_final: 0.8351 (mt) REVERT: H 483 MET cc_start: 0.9181 (tmm) cc_final: 0.8827 (tmm) outliers start: 80 outliers final: 60 residues processed: 778 average time/residue: 0.1468 time to fit residues: 181.9984 Evaluate side-chains 741 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 679 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 43 ASP Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 437 ILE Chi-restraints excluded: chain H residue 505 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 0 optimal weight: 6.9990 chunk 192 optimal weight: 0.9990 chunk 239 optimal weight: 3.9990 chunk 262 optimal weight: 0.7980 chunk 148 optimal weight: 0.0020 chunk 106 optimal weight: 0.9990 chunk 253 optimal weight: 0.4980 chunk 64 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 chunk 225 optimal weight: 0.4980 chunk 200 optimal weight: 5.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 GLN D 465 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.151175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.126154 restraints weight = 32458.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.131107 restraints weight = 16803.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.134516 restraints weight = 10454.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.136843 restraints weight = 7353.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.138484 restraints weight = 5665.678| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23488 Z= 0.131 Angle : 0.686 10.383 31792 Z= 0.341 Chirality : 0.045 0.226 3656 Planarity : 0.004 0.059 4000 Dihedral : 8.400 87.196 3736 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.61 % Allowed : 31.54 % Favored : 64.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.15), residues: 2960 helix: 0.18 (0.16), residues: 1016 sheet: -2.42 (0.29), residues: 304 loop : -0.78 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 356 TYR 0.024 0.002 TYR B 12 PHE 0.015 0.001 PHE D 44 HIS 0.010 0.001 HIS F 92 Details of bonding type rmsd covalent geometry : bond 0.00309 (23480) covalent geometry : angle 0.68562 (31792) hydrogen bonds : bond 0.02842 ( 784) hydrogen bonds : angle 4.75683 ( 2256) Misc. bond : bond 0.00029 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 729 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 5 LEU cc_start: 0.9032 (pt) cc_final: 0.8706 (pt) REVERT: A 43 ASP cc_start: 0.7812 (m-30) cc_final: 0.7465 (m-30) REVERT: A 78 MET cc_start: 0.8464 (tpp) cc_final: 0.8195 (tpp) REVERT: A 102 ASN cc_start: 0.8786 (t0) cc_final: 0.8118 (t0) REVERT: A 259 ARG cc_start: 0.8907 (tpp80) cc_final: 0.8528 (tpp80) REVERT: A 274 ASP cc_start: 0.8712 (t0) cc_final: 0.8228 (t70) REVERT: A 312 ASN cc_start: 0.9138 (m110) cc_final: 0.8553 (m-40) REVERT: A 386 MET cc_start: 0.9360 (ptp) cc_final: 0.8761 (pmm) REVERT: A 441 GLN cc_start: 0.8714 (mt0) cc_final: 0.8400 (mt0) REVERT: A 465 GLN cc_start: 0.8848 (mm110) cc_final: 0.8498 (mm-40) REVERT: A 483 MET cc_start: 0.9192 (tmm) cc_final: 0.8702 (tmm) REVERT: B 5 LEU cc_start: 0.9055 (pt) cc_final: 0.8699 (pt) REVERT: B 75 GLU cc_start: 0.7844 (tp30) cc_final: 0.7467 (tp30) REVERT: B 92 HIS cc_start: 0.8754 (p-80) cc_final: 0.8266 (p90) REVERT: B 102 ASN cc_start: 0.8933 (t0) cc_final: 0.8313 (t0) REVERT: B 242 LYS cc_start: 0.8416 (mttp) cc_final: 0.8019 (tppt) REVERT: B 259 ARG cc_start: 0.8795 (ttm-80) cc_final: 0.8343 (tpp80) REVERT: B 274 ASP cc_start: 0.8774 (t0) cc_final: 0.8368 (t70) REVERT: B 441 GLN cc_start: 0.8667 (mt0) cc_final: 0.8435 (mt0) REVERT: B 461 ILE cc_start: 0.8779 (pt) cc_final: 0.8447 (mt) REVERT: B 491 GLU cc_start: 0.8743 (tp30) cc_final: 0.8385 (tp30) REVERT: C 50 ASP cc_start: 0.8289 (t0) cc_final: 0.8059 (t0) REVERT: C 51 LEU cc_start: 0.9121 (tt) cc_final: 0.8620 (tp) REVERT: C 68 SER cc_start: 0.9256 (p) cc_final: 0.9019 (p) REVERT: C 75 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7429 (mm-30) REVERT: C 78 MET cc_start: 0.8238 (tpp) cc_final: 0.8022 (tpp) REVERT: C 102 ASN cc_start: 0.8747 (t0) cc_final: 0.8055 (t0) REVERT: C 259 ARG cc_start: 0.8743 (tpp80) cc_final: 0.8471 (tpp80) REVERT: C 274 ASP cc_start: 0.8764 (t0) cc_final: 0.8237 (t70) REVERT: C 441 GLN cc_start: 0.8701 (mt0) cc_final: 0.8370 (mt0) REVERT: C 465 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8498 (mm110) REVERT: C 483 MET cc_start: 0.9225 (tmm) cc_final: 0.8799 (tmm) REVERT: D 59 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7536 (pt) REVERT: D 92 HIS cc_start: 0.8638 (p-80) cc_final: 0.8280 (p90) REVERT: D 102 ASN cc_start: 0.9007 (t0) cc_final: 0.8522 (t0) REVERT: D 259 ARG cc_start: 0.8845 (tpp80) cc_final: 0.8476 (tpp80) REVERT: D 274 ASP cc_start: 0.8781 (t0) cc_final: 0.8128 (t70) REVERT: D 355 ARG cc_start: 0.8713 (ttp-170) cc_final: 0.8445 (ttp-170) REVERT: D 399 GLU cc_start: 0.7897 (mp0) cc_final: 0.7650 (mp0) REVERT: D 441 GLN cc_start: 0.8630 (mt0) cc_final: 0.8292 (mt0) REVERT: D 448 GLN cc_start: 0.7615 (pt0) cc_final: 0.7413 (pt0) REVERT: D 461 ILE cc_start: 0.8803 (pt) cc_final: 0.8216 (mt) REVERT: D 465 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8416 (mm110) REVERT: D 483 MET cc_start: 0.9213 (tmm) cc_final: 0.8799 (tmm) REVERT: E 43 ASP cc_start: 0.8156 (m-30) cc_final: 0.7850 (m-30) REVERT: E 68 SER cc_start: 0.9213 (p) cc_final: 0.8990 (p) REVERT: E 102 ASN cc_start: 0.8710 (t0) cc_final: 0.8026 (t0) REVERT: E 441 GLN cc_start: 0.8737 (mt0) cc_final: 0.8453 (mt0) REVERT: E 483 MET cc_start: 0.9210 (tmm) cc_final: 0.8729 (tmm) REVERT: E 491 GLU cc_start: 0.8769 (tp30) cc_final: 0.8486 (tp30) REVERT: F 102 ASN cc_start: 0.8934 (t0) cc_final: 0.8367 (t0) REVERT: F 285 ASN cc_start: 0.9129 (m110) cc_final: 0.8757 (m-40) REVERT: F 441 GLN cc_start: 0.8681 (mt0) cc_final: 0.8350 (mt0) REVERT: F 461 ILE cc_start: 0.8870 (pt) cc_final: 0.8391 (mt) REVERT: F 483 MET cc_start: 0.9171 (tmm) cc_final: 0.8797 (tmm) REVERT: G 75 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7554 (mm-30) REVERT: G 102 ASN cc_start: 0.8800 (t0) cc_final: 0.8128 (t0) REVERT: G 259 ARG cc_start: 0.8824 (tpp80) cc_final: 0.8575 (ttp-170) REVERT: G 274 ASP cc_start: 0.8834 (t0) cc_final: 0.8324 (t70) REVERT: G 312 ASN cc_start: 0.9239 (m-40) cc_final: 0.8669 (m-40) REVERT: G 441 GLN cc_start: 0.8730 (mt0) cc_final: 0.8461 (mt0) REVERT: G 483 MET cc_start: 0.9184 (tmm) cc_final: 0.8777 (tmm) REVERT: H 92 HIS cc_start: 0.8661 (p-80) cc_final: 0.8320 (p90) REVERT: H 102 ASN cc_start: 0.9017 (t0) cc_final: 0.8547 (t0) REVERT: H 242 LYS cc_start: 0.8355 (mttp) cc_final: 0.8020 (tppt) REVERT: H 258 TYR cc_start: 0.8422 (t80) cc_final: 0.8202 (t80) REVERT: H 259 ARG cc_start: 0.8777 (tpp80) cc_final: 0.8284 (tpp80) REVERT: H 274 ASP cc_start: 0.8780 (t0) cc_final: 0.7990 (t70) REVERT: H 441 GLN cc_start: 0.8685 (mt0) cc_final: 0.8366 (mt0) REVERT: H 461 ILE cc_start: 0.8722 (pt) cc_final: 0.8245 (mt) REVERT: H 465 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8323 (mm110) outliers start: 86 outliers final: 64 residues processed: 793 average time/residue: 0.1454 time to fit residues: 182.9352 Evaluate side-chains 763 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 695 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 505 SER Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 43 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 345 THR Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 437 ILE Chi-restraints excluded: chain H residue 465 GLN Chi-restraints excluded: chain H residue 505 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 168 optimal weight: 4.9990 chunk 218 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 283 optimal weight: 0.0370 chunk 165 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 181 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 77 optimal weight: 0.0670 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 GLN C 465 GLN ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 GLN ** G 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.149092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.125432 restraints weight = 32182.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.130107 restraints weight = 16770.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.133422 restraints weight = 10445.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.135581 restraints weight = 7325.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.137077 restraints weight = 5629.991| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23488 Z= 0.165 Angle : 0.714 10.111 31792 Z= 0.357 Chirality : 0.046 0.197 3656 Planarity : 0.004 0.065 4000 Dihedral : 8.315 87.222 3733 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.48 % Allowed : 32.01 % Favored : 64.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.16), residues: 2960 helix: 0.03 (0.15), residues: 1072 sheet: -2.33 (0.29), residues: 304 loop : -0.79 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 355 TYR 0.041 0.002 TYR B 484 PHE 0.012 0.001 PHE D 44 HIS 0.011 0.001 HIS F 92 Details of bonding type rmsd covalent geometry : bond 0.00399 (23480) covalent geometry : angle 0.71427 (31792) hydrogen bonds : bond 0.02991 ( 784) hydrogen bonds : angle 4.75706 ( 2256) Misc. bond : bond 0.00097 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 698 time to evaluate : 0.823 Fit side-chains REVERT: A 5 LEU cc_start: 0.8939 (pt) cc_final: 0.8624 (pt) REVERT: A 43 ASP cc_start: 0.7727 (m-30) cc_final: 0.7305 (m-30) REVERT: A 102 ASN cc_start: 0.8767 (t0) cc_final: 0.8114 (t0) REVERT: A 259 ARG cc_start: 0.8893 (tpp80) cc_final: 0.8542 (tpp80) REVERT: A 274 ASP cc_start: 0.8808 (t0) cc_final: 0.8422 (t70) REVERT: A 312 ASN cc_start: 0.9156 (m110) cc_final: 0.8610 (m-40) REVERT: A 441 GLN cc_start: 0.8633 (mt0) cc_final: 0.8430 (mt0) REVERT: A 465 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8462 (mm-40) REVERT: A 483 MET cc_start: 0.9170 (tmm) cc_final: 0.8739 (tmm) REVERT: A 491 GLU cc_start: 0.8701 (tp30) cc_final: 0.8489 (tp30) REVERT: B 5 LEU cc_start: 0.8969 (pt) cc_final: 0.8721 (pt) REVERT: B 75 GLU cc_start: 0.7823 (tp30) cc_final: 0.7523 (tp30) REVERT: B 92 HIS cc_start: 0.8677 (p-80) cc_final: 0.8229 (p90) REVERT: B 102 ASN cc_start: 0.8913 (t0) cc_final: 0.8278 (t0) REVERT: B 242 LYS cc_start: 0.8433 (mttp) cc_final: 0.8028 (tppt) REVERT: B 259 ARG cc_start: 0.8734 (ttm-80) cc_final: 0.8371 (tpp80) REVERT: B 274 ASP cc_start: 0.8867 (t0) cc_final: 0.8296 (t70) REVERT: B 441 GLN cc_start: 0.8652 (mt0) cc_final: 0.8431 (mt0) REVERT: B 461 ILE cc_start: 0.8849 (pt) cc_final: 0.8533 (mt) REVERT: B 491 GLU cc_start: 0.8793 (tp30) cc_final: 0.8449 (tp30) REVERT: C 51 LEU cc_start: 0.9075 (tt) cc_final: 0.8688 (tp) REVERT: C 102 ASN cc_start: 0.8782 (t0) cc_final: 0.8085 (t0) REVERT: C 259 ARG cc_start: 0.8721 (tpp80) cc_final: 0.8472 (tpp80) REVERT: C 274 ASP cc_start: 0.8789 (t0) cc_final: 0.8349 (t70) REVERT: C 441 GLN cc_start: 0.8673 (mt0) cc_final: 0.8402 (mt0) REVERT: C 465 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8582 (mm-40) REVERT: C 483 MET cc_start: 0.9123 (tmm) cc_final: 0.8744 (tmm) REVERT: D 59 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7670 (pt) REVERT: D 92 HIS cc_start: 0.8639 (p-80) cc_final: 0.8331 (p90) REVERT: D 102 ASN cc_start: 0.8940 (t0) cc_final: 0.8433 (t0) REVERT: D 259 ARG cc_start: 0.8817 (tpp80) cc_final: 0.8465 (tpp80) REVERT: D 274 ASP cc_start: 0.8875 (t0) cc_final: 0.8348 (t70) REVERT: D 355 ARG cc_start: 0.8822 (ttp-170) cc_final: 0.8546 (ttp-170) REVERT: D 386 MET cc_start: 0.9124 (ptp) cc_final: 0.8829 (ptp) REVERT: D 399 GLU cc_start: 0.7889 (mp0) cc_final: 0.7668 (mp0) REVERT: D 441 GLN cc_start: 0.8609 (mt0) cc_final: 0.8344 (mt0) REVERT: D 465 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8560 (mm-40) REVERT: D 483 MET cc_start: 0.9191 (tmm) cc_final: 0.8768 (tmm) REVERT: E 43 ASP cc_start: 0.7941 (m-30) cc_final: 0.7635 (m-30) REVERT: E 102 ASN cc_start: 0.8674 (t0) cc_final: 0.7979 (t0) REVERT: E 441 GLN cc_start: 0.8701 (mt0) cc_final: 0.8467 (mt0) REVERT: E 483 MET cc_start: 0.9093 (tmm) cc_final: 0.8882 (tmm) REVERT: E 491 GLU cc_start: 0.8831 (tp30) cc_final: 0.8576 (tp30) REVERT: F 102 ASN cc_start: 0.8872 (t0) cc_final: 0.8290 (t0) REVERT: F 441 GLN cc_start: 0.8621 (mt0) cc_final: 0.8366 (mt0) REVERT: F 461 ILE cc_start: 0.8994 (pt) cc_final: 0.8487 (mt) REVERT: G 75 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7583 (mm-30) REVERT: G 102 ASN cc_start: 0.8732 (t0) cc_final: 0.8068 (t0) REVERT: G 259 ARG cc_start: 0.8778 (tpp80) cc_final: 0.8476 (ttp-170) REVERT: G 274 ASP cc_start: 0.8874 (t0) cc_final: 0.8470 (t70) REVERT: G 312 ASN cc_start: 0.9239 (m-40) cc_final: 0.8678 (m-40) REVERT: G 441 GLN cc_start: 0.8646 (mt0) cc_final: 0.8412 (mt0) REVERT: G 483 MET cc_start: 0.9152 (tmm) cc_final: 0.8764 (tmm) REVERT: H 92 HIS cc_start: 0.8638 (p-80) cc_final: 0.8240 (p90) REVERT: H 102 ASN cc_start: 0.9030 (t0) cc_final: 0.8493 (t0) REVERT: H 242 LYS cc_start: 0.8368 (mttp) cc_final: 0.8051 (tppt) REVERT: H 258 TYR cc_start: 0.8405 (t80) cc_final: 0.8165 (t80) REVERT: H 259 ARG cc_start: 0.8735 (tpp80) cc_final: 0.8466 (tpp80) REVERT: H 274 ASP cc_start: 0.8875 (t0) cc_final: 0.8164 (t70) REVERT: H 461 ILE cc_start: 0.8830 (pt) cc_final: 0.8353 (mt) REVERT: H 465 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8432 (mm110) outliers start: 83 outliers final: 72 residues processed: 758 average time/residue: 0.1518 time to fit residues: 181.4741 Evaluate side-chains 756 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 679 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 505 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 505 SER Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 43 ASP Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 345 THR Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 465 GLN Chi-restraints excluded: chain H residue 505 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 99 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 130 optimal weight: 0.0770 chunk 256 optimal weight: 0.6980 chunk 179 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 170 optimal weight: 0.6980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 GLN ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.145477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.120682 restraints weight = 32167.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.125553 restraints weight = 16570.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.128945 restraints weight = 10256.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.131126 restraints weight = 7171.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.132862 restraints weight = 5513.174| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 23488 Z= 0.138 Angle : 0.704 9.874 31792 Z= 0.351 Chirality : 0.045 0.268 3656 Planarity : 0.004 0.066 4000 Dihedral : 8.141 87.017 3730 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.44 % Allowed : 32.26 % Favored : 64.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.15), residues: 2960 helix: 0.30 (0.16), residues: 1016 sheet: -2.26 (0.29), residues: 304 loop : -0.68 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 355 TYR 0.042 0.002 TYR B 484 PHE 0.013 0.001 PHE D 44 HIS 0.010 0.001 HIS F 92 Details of bonding type rmsd covalent geometry : bond 0.00332 (23480) covalent geometry : angle 0.70434 (31792) hydrogen bonds : bond 0.02954 ( 784) hydrogen bonds : angle 4.76385 ( 2256) Misc. bond : bond 0.00043 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4189.26 seconds wall clock time: 73 minutes 16.96 seconds (4396.96 seconds total)