Starting phenix.real_space_refine on Sun Sep 13 12:01:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ua5_20706/09_2026/6ua5_20706.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ua5_20706/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6ua5_20706/09_2026/6ua5_20706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ua5_20706/09_2026/6ua5_20706.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6ua5_20706/09_2026/6ua5_20706.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ua5_20706/09_2026/6ua5_20706.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ua5_20706/09_2026/6ua5_20706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ua5_20706/09_2026/6ua5_20706.map" } 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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 4.36, per 1000 atoms: 0.19 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: 1.34 Conformation dependent library (CDL) restraints added in 892.3 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: 0.61 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: 3.24 Time building geometry restraints manager: 1.95 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: 30341 3.21 - 6.42: 1171 6.42 - 9.63: 208 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: 12679 17.11 - 34.23: 785 34.23 - 51.34: 284 51.34 - 68.46: 88 68.46 - 85.57: 12 Dihedral angle restraints: 13848 sinusoidal: 5344 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 13845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2508 0.067 - 0.134: 873 0.134 - 0.201: 218 0.201 - 0.268: 30 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: 1.110 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: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 17.660 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 : 1.518 16.046 31792 Z= 0.769 Chirality : 0.075 0.335 3656 Planarity : 0.007 0.058 4000 Dihedral : 14.103 85.571 8456 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/Z covalent geometry : bond 0.01429 / 0.66 (23480) covalent geometry : angle 1.51776 / 0.77 (31792) hydrogen bonds : bond 0.18889 / 12.54 ( 784) hydrogen bonds : angle 7.95625 / 5.46 ( 2256) Misc. bond : bond 0.00325 / 0.16 ( 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 : 0.842 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: 0.1456 time to fit residues: 229.4599 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 : 0.850 ------------------------------------------------------------------------------- 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... ** 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 = 0.3705 r_free = 0.3705 target = 0.153569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.127272 restraints weight = 33357.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.132358 restraints weight = 17085.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.135899 restraints weight = 10735.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.138196 restraints weight = 7637.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.139854 restraints weight = 5976.287| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23488 Z= 0.144 Angle : 0.709 11.495 31792 Z= 0.358 Chirality : 0.047 0.173 3656 Planarity : 0.005 0.037 4000 Dihedral : 10.972 81.228 3544 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.12 % Allowed : 18.58 % Favored : 76.30 % 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: -2.76 (0.14), residues: 2960 helix: -2.31 (0.13), residues: 1000 sheet: -2.36 (0.23), residues: 432 loop : -1.18 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 407 TYR 0.016 0.002 TYR B 41 PHE 0.017 0.002 PHE H 44 HIS 0.006 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (23480) covalent geometry : angle 0.70947 / 0.36 (31792) hydrogen bonds : bond 0.03341 / 2.19 ( 784) hydrogen bonds : angle 5.73271 / 3.94 ( 2256) Misc. bond : bond 0.00021 / 0.01 ( 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 936 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 814 time to evaluate : 0.869 Fit side-chains REVERT: A 42 ILE cc_start: 0.8006 (pt) cc_final: 0.7764 (pt) REVERT: A 102 ASN cc_start: 0.8440 (t0) cc_final: 0.7761 (t0) REVERT: A 258 TYR cc_start: 0.8580 (t80) cc_final: 0.8374 (t80) REVERT: A 274 ASP cc_start: 0.8871 (t0) cc_final: 0.8604 (t70) REVERT: A 327 SER cc_start: 0.8676 (p) cc_final: 0.8228 (p) REVERT: B 102 ASN cc_start: 0.8599 (t0) cc_final: 0.7962 (t0) REVERT: B 241 LYS cc_start: 0.9073 (tppt) cc_final: 0.8838 (tppt) REVERT: B 274 ASP cc_start: 0.8906 (t0) cc_final: 0.8554 (t70) REVERT: B 461 ILE cc_start: 0.8935 (pt) cc_final: 0.8576 (mt) REVERT: B 483 MET cc_start: 0.9115 (tmm) cc_final: 0.8648 (tmm) REVERT: C 56 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8476 (p) REVERT: C 102 ASN cc_start: 0.8503 (t0) cc_final: 0.7732 (t0) REVERT: C 103 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7989 (tp30) REVERT: C 274 ASP cc_start: 0.8836 (t0) cc_final: 0.8582 (t70) REVERT: C 296 ASN cc_start: 0.8532 (p0) cc_final: 0.8247 (p0) REVERT: C 327 SER cc_start: 0.8558 (p) cc_final: 0.8127 (p) REVERT: C 461 ILE cc_start: 0.9002 (pt) cc_final: 0.8593 (mt) REVERT: C 491 GLU cc_start: 0.8535 (tp30) cc_final: 0.8334 (tp30) REVERT: D 56 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8420 (p) REVERT: D 102 ASN cc_start: 0.8675 (t0) cc_final: 0.7957 (t0) REVERT: D 103 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8239 (tp30) REVERT: D 274 ASP cc_start: 0.8921 (t0) cc_final: 0.8605 (t70) REVERT: D 296 ASN cc_start: 0.8584 (p0) cc_final: 0.8249 (p0) REVERT: D 359 VAL cc_start: 0.9355 (t) cc_final: 0.9038 (p) REVERT: D 395 GLU cc_start: 0.8667 (mp0) cc_final: 0.8400 (mp0) REVERT: D 409 LYS cc_start: 0.8456 (ptpt) cc_final: 0.8251 (ptpt) REVERT: D 461 ILE cc_start: 0.8943 (pt) cc_final: 0.8520 (mt) REVERT: D 483 MET cc_start: 0.9162 (tmm) cc_final: 0.8627 (tmm) REVERT: E 42 ILE cc_start: 0.8140 (pt) cc_final: 0.7877 (pt) REVERT: E 43 ASP cc_start: 0.7707 (m-30) cc_final: 0.7503 (m-30) REVERT: E 102 ASN cc_start: 0.8438 (t0) cc_final: 0.7697 (t0) REVERT: E 103 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7879 (tp30) REVERT: E 269 ASP cc_start: 0.8678 (m-30) cc_final: 0.7995 (m-30) REVERT: E 296 ASN cc_start: 0.8568 (p0) cc_final: 0.8185 (p0) REVERT: E 327 SER cc_start: 0.8738 (p) cc_final: 0.8296 (p) REVERT: E 399 GLU cc_start: 0.8067 (pm20) cc_final: 0.7772 (pp20) REVERT: E 483 MET cc_start: 0.9210 (tmm) cc_final: 0.8585 (tmm) REVERT: F 82 MET cc_start: 0.8720 (mtp) cc_final: 0.8453 (mtp) REVERT: F 102 ASN cc_start: 0.8718 (t0) cc_final: 0.8067 (t0) REVERT: F 103 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8334 (tp30) REVERT: F 258 TYR cc_start: 0.8684 (t80) cc_final: 0.8450 (t80) REVERT: F 259 ARG cc_start: 0.8553 (ttm-80) cc_final: 0.8108 (tpp80) REVERT: F 285 ASN cc_start: 0.8825 (m110) cc_final: 0.8591 (m110) REVERT: F 296 ASN cc_start: 0.8690 (p0) cc_final: 0.8280 (p0) REVERT: F 319 ASP cc_start: 0.8085 (t0) cc_final: 0.7871 (t0) REVERT: F 327 SER cc_start: 0.8728 (p) cc_final: 0.8317 (p) REVERT: F 461 ILE cc_start: 0.8951 (pt) cc_final: 0.8574 (mt) REVERT: F 483 MET cc_start: 0.9165 (tmm) cc_final: 0.8617 (tmm) REVERT: G 102 ASN cc_start: 0.8409 (t0) cc_final: 0.7674 (t0) REVERT: G 259 ARG cc_start: 0.8614 (ttm-80) cc_final: 0.8103 (ttm110) REVERT: G 274 ASP cc_start: 0.8919 (t0) cc_final: 0.8650 (t70) REVERT: G 296 ASN cc_start: 0.8569 (p0) cc_final: 0.8266 (p0) REVERT: G 327 SER cc_start: 0.8722 (p) cc_final: 0.8268 (p) REVERT: G 395 GLU cc_start: 0.8616 (mp0) cc_final: 0.8239 (mp0) REVERT: G 453 ILE cc_start: 0.8997 (pp) cc_final: 0.8766 (pt) REVERT: G 461 ILE cc_start: 0.8897 (pt) cc_final: 0.8487 (mt) REVERT: G 483 MET cc_start: 0.9122 (tmm) cc_final: 0.8607 (tmm) REVERT: G 491 GLU cc_start: 0.8384 (tp30) cc_final: 0.8166 (tp30) REVERT: H 102 ASN cc_start: 0.8633 (t0) cc_final: 0.7967 (t0) REVERT: H 241 LYS cc_start: 0.9171 (tppt) cc_final: 0.8959 (tppt) REVERT: H 258 TYR cc_start: 0.8657 (t80) cc_final: 0.8407 (t80) REVERT: H 274 ASP cc_start: 0.8835 (t0) cc_final: 0.8299 (t70) REVERT: H 296 ASN cc_start: 0.8535 (p0) cc_final: 0.8210 (p0) REVERT: H 395 GLU cc_start: 0.8696 (mp0) cc_final: 0.8294 (mp0) REVERT: H 461 ILE cc_start: 0.8889 (pt) cc_final: 0.8466 (mt) REVERT: H 483 MET cc_start: 0.9127 (tmm) cc_final: 0.8581 (tmm) outliers start: 122 outliers final: 52 residues processed: 863 average time/residue: 0.1418 time to fit residues: 195.2703 Evaluate side-chains 759 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 701 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 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 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 103 GLU 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 103 GLU Chi-restraints excluded: chain F residue 245 LEU 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 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 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: 2.9990 chunk 152 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 262 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 248 optimal weight: 0.7980 chunk 179 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 GLN ** 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** D 283 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 ASN E 298 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.152953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.126443 restraints weight = 33243.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.131557 restraints weight = 17090.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.134916 restraints weight = 10750.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.137308 restraints weight = 7736.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.138925 restraints weight = 6080.785| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23488 Z= 0.147 Angle : 0.703 13.176 31792 Z= 0.344 Chirality : 0.048 0.150 3656 Planarity : 0.005 0.066 4000 Dihedral : 8.972 85.438 3400 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.27 % Allowed : 24.16 % Favored : 72.57 % 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: -2.24 (0.15), residues: 2960 helix: -1.46 (0.14), residues: 1048 sheet: -2.42 (0.23), residues: 432 loop : -1.06 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 355 TYR 0.028 0.002 TYR A 289 PHE 0.014 0.002 PHE D 44 HIS 0.008 0.001 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (23480) covalent geometry : angle 0.70255 / 0.34 (31792) hydrogen bonds : bond 0.03250 / 2.14 ( 784) hydrogen bonds : angle 5.22079 / 3.60 ( 2256) Misc. bond : bond 0.00016 / 0.01 ( 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 849 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 771 time to evaluate : 0.744 Fit side-chains REVERT: A 42 ILE cc_start: 0.8296 (pt) cc_final: 0.8089 (pt) REVERT: A 102 ASN cc_start: 0.8498 (t0) cc_final: 0.7792 (t0) REVERT: A 259 ARG cc_start: 0.8927 (tpp80) cc_final: 0.8575 (tpp80) REVERT: A 274 ASP cc_start: 0.8833 (t0) cc_final: 0.8608 (t70) REVERT: A 441 GLN cc_start: 0.8613 (mt0) cc_final: 0.8302 (mt0) REVERT: A 483 MET cc_start: 0.9124 (tmm) cc_final: 0.8640 (tmm) REVERT: B 51 LEU cc_start: 0.9046 (tt) cc_final: 0.8350 (tt) REVERT: B 102 ASN cc_start: 0.8643 (t0) cc_final: 0.7955 (t0) REVERT: B 274 ASP cc_start: 0.8899 (t0) cc_final: 0.8562 (t70) REVERT: B 399 GLU cc_start: 0.8074 (pm20) cc_final: 0.7865 (mp0) REVERT: B 461 ILE cc_start: 0.8932 (pt) cc_final: 0.8550 (mt) REVERT: B 483 MET cc_start: 0.9160 (tmm) cc_final: 0.8698 (tmm) REVERT: C 102 ASN cc_start: 0.8606 (t0) cc_final: 0.7862 (t0) REVERT: C 254 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7622 (tt0) REVERT: C 259 ARG cc_start: 0.8877 (tpp80) cc_final: 0.8602 (tpp80) REVERT: C 274 ASP cc_start: 0.8844 (t0) cc_final: 0.8613 (t70) REVERT: C 327 SER cc_start: 0.8478 (p) cc_final: 0.8091 (p) REVERT: C 461 ILE cc_start: 0.8889 (pt) cc_final: 0.8579 (mt) REVERT: C 483 MET cc_start: 0.9164 (tmm) cc_final: 0.8633 (tmm) REVERT: D 56 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8480 (p) REVERT: D 102 ASN cc_start: 0.8723 (t0) cc_final: 0.8027 (t0) REVERT: D 274 ASP cc_start: 0.8870 (t0) cc_final: 0.8622 (t70) REVERT: D 461 ILE cc_start: 0.8910 (pt) cc_final: 0.8540 (mt) REVERT: D 483 MET cc_start: 0.9173 (tmm) cc_final: 0.8638 (tmm) REVERT: E 42 ILE cc_start: 0.8387 (pt) cc_final: 0.8008 (pt) REVERT: E 43 ASP cc_start: 0.7902 (m-30) cc_final: 0.7646 (m-30) REVERT: E 102 ASN cc_start: 0.8551 (t0) cc_final: 0.7833 (t0) REVERT: E 259 ARG cc_start: 0.8846 (tpp80) cc_final: 0.8501 (tpp80) REVERT: E 296 ASN cc_start: 0.8521 (p0) cc_final: 0.8194 (p0) REVERT: E 327 SER cc_start: 0.8505 (p) cc_final: 0.8145 (p) REVERT: E 441 GLN cc_start: 0.8600 (mt0) cc_final: 0.8363 (mt0) REVERT: E 483 MET cc_start: 0.9181 (tmm) cc_final: 0.8747 (tmm) REVERT: F 78 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7796 (ttp) REVERT: F 102 ASN cc_start: 0.8848 (t0) cc_final: 0.8176 (t0) REVERT: F 259 ARG cc_start: 0.8635 (ttm-80) cc_final: 0.8092 (tpp80) REVERT: F 285 ASN cc_start: 0.8903 (m110) cc_final: 0.8630 (m110) REVERT: F 296 ASN cc_start: 0.8626 (p0) cc_final: 0.8238 (p0) REVERT: F 461 ILE cc_start: 0.8923 (pt) cc_final: 0.8593 (mt) REVERT: F 491 GLU cc_start: 0.8488 (tp30) cc_final: 0.8268 (tp30) REVERT: G 102 ASN cc_start: 0.8512 (t0) cc_final: 0.7739 (t0) REVERT: G 259 ARG cc_start: 0.8565 (ttm-80) cc_final: 0.8229 (tpp80) REVERT: G 274 ASP cc_start: 0.8914 (t0) cc_final: 0.8641 (t70) REVERT: G 327 SER cc_start: 0.8480 (p) cc_final: 0.8081 (p) REVERT: G 395 GLU cc_start: 0.8517 (mp0) cc_final: 0.8132 (mp0) REVERT: G 409 LYS cc_start: 0.8367 (ptpt) cc_final: 0.8134 (ptpt) REVERT: G 441 GLN cc_start: 0.8599 (mt0) cc_final: 0.8301 (mt0) REVERT: G 461 ILE cc_start: 0.8862 (pt) cc_final: 0.8518 (mt) REVERT: G 483 MET cc_start: 0.9218 (tmm) cc_final: 0.8765 (tmm) REVERT: H 75 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7323 (mm-30) REVERT: H 82 MET cc_start: 0.8803 (mtp) cc_final: 0.8592 (mtp) REVERT: H 102 ASN cc_start: 0.8810 (t0) cc_final: 0.8140 (t0) REVERT: H 242 LYS cc_start: 0.8292 (mttp) cc_final: 0.7961 (tppt) REVERT: H 259 ARG cc_start: 0.8901 (tpp80) cc_final: 0.8394 (tpp80) REVERT: H 274 ASP cc_start: 0.8855 (t0) cc_final: 0.8406 (t70) REVERT: H 395 GLU cc_start: 0.8633 (mp0) cc_final: 0.8387 (mp0) REVERT: H 461 ILE cc_start: 0.8868 (pt) cc_final: 0.8497 (mt) REVERT: H 483 MET cc_start: 0.9181 (tmm) cc_final: 0.8717 (tmm) outliers start: 78 outliers final: 41 residues processed: 804 average time/residue: 0.1431 time to fit residues: 183.9314 Evaluate side-chains 719 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 675 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 275 SER 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 254 GLU 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 306 THR 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 78 MET Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 275 SER 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 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 312 ASN Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 500 GLU 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 500 GLU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 271 VAL 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: 0.7980 chunk 275 optimal weight: 7.9990 chunk 225 optimal weight: 0.6980 chunk 145 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 280 optimal weight: 0.8980 chunk 219 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 228 optimal weight: 0.0470 chunk 214 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 B 243 GLN B 298 GLN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN ** 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 ** D 309 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 277 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 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** 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** H 312 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.154658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.127982 restraints weight = 33227.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.133041 restraints weight = 17235.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.136524 restraints weight = 10941.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.138848 restraints weight = 7876.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.140379 restraints weight = 6197.911| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23488 Z= 0.131 Angle : 0.658 9.804 31792 Z= 0.326 Chirality : 0.046 0.145 3656 Planarity : 0.004 0.047 4000 Dihedral : 8.155 87.544 3360 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.03 % Allowed : 26.97 % Favored : 69.00 % 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: -1.81 (0.15), residues: 2960 helix: -0.91 (0.15), residues: 1008 sheet: -2.42 (0.22), residues: 432 loop : -0.89 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 355 TYR 0.022 0.002 TYR F 4 PHE 0.012 0.001 PHE C 44 HIS 0.009 0.001 HIS F 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (23480) covalent geometry : angle 0.65774 / 0.33 (31792) hydrogen bonds : bond 0.02957 / 1.93 ( 784) hydrogen bonds : angle 5.02060 / 3.45 ( 2256) Misc. bond : bond 0.00017 / 0.01 ( 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 838 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 742 time to evaluate : 0.791 Fit side-chains REVERT: A 102 ASN cc_start: 0.8598 (t0) cc_final: 0.7864 (t0) REVERT: A 259 ARG cc_start: 0.8862 (tpp80) cc_final: 0.8334 (tpp80) REVERT: A 399 GLU cc_start: 0.7740 (mp0) cc_final: 0.7483 (mp0) REVERT: A 441 GLN cc_start: 0.8641 (mt0) cc_final: 0.8330 (mt0) REVERT: A 483 MET cc_start: 0.9152 (tmm) cc_final: 0.8693 (tmm) REVERT: B 92 HIS cc_start: 0.8572 (p-80) cc_final: 0.8336 (p90) REVERT: B 102 ASN cc_start: 0.8722 (t0) cc_final: 0.8073 (t0) REVERT: B 242 LYS cc_start: 0.8255 (mttp) cc_final: 0.7953 (tppt) REVERT: B 274 ASP cc_start: 0.8904 (t0) cc_final: 0.8636 (t70) REVERT: B 399 GLU cc_start: 0.8002 (pm20) cc_final: 0.7769 (mp0) REVERT: B 461 ILE cc_start: 0.8872 (pt) cc_final: 0.8599 (mt) REVERT: B 483 MET cc_start: 0.9175 (tmm) cc_final: 0.8700 (tmm) REVERT: B 491 GLU cc_start: 0.8535 (tp30) cc_final: 0.8246 (tp30) REVERT: C 78 MET cc_start: 0.7813 (tpt) cc_final: 0.7271 (tpt) REVERT: C 102 ASN cc_start: 0.8697 (t0) cc_final: 0.7939 (t0) REVERT: C 259 ARG cc_start: 0.8882 (tpp80) cc_final: 0.8572 (tpp80) REVERT: C 461 ILE cc_start: 0.8888 (pt) cc_final: 0.8623 (mt) REVERT: C 483 MET cc_start: 0.9180 (tmm) cc_final: 0.8675 (tmm) REVERT: D 56 THR cc_start: 0.8550 (OUTLIER) cc_final: 0.8263 (p) REVERT: D 59 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7774 (pt) REVERT: D 92 HIS cc_start: 0.8495 (p-80) cc_final: 0.8295 (p90) REVERT: D 102 ASN cc_start: 0.8858 (t0) cc_final: 0.8182 (t0) REVERT: D 274 ASP cc_start: 0.8905 (t0) cc_final: 0.8631 (t70) REVERT: D 461 ILE cc_start: 0.8865 (pt) cc_final: 0.8539 (mt) REVERT: D 483 MET cc_start: 0.9172 (tmm) cc_final: 0.8647 (tmm) REVERT: E 43 ASP cc_start: 0.7906 (m-30) cc_final: 0.7674 (m-30) REVERT: E 102 ASN cc_start: 0.8635 (t0) cc_final: 0.7878 (t0) REVERT: E 258 TYR cc_start: 0.8518 (t80) cc_final: 0.8258 (t80) REVERT: E 259 ARG cc_start: 0.8859 (tpp80) cc_final: 0.8310 (tpp80) REVERT: E 296 ASN cc_start: 0.8471 (p0) cc_final: 0.8173 (p0) REVERT: E 441 GLN cc_start: 0.8676 (mt0) cc_final: 0.8414 (mt0) REVERT: E 453 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8407 (pt) REVERT: E 483 MET cc_start: 0.9180 (tmm) cc_final: 0.8676 (tmm) REVERT: E 491 GLU cc_start: 0.8653 (tp30) cc_final: 0.8416 (tp30) REVERT: F 78 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7575 (ttp) REVERT: F 102 ASN cc_start: 0.8865 (t0) cc_final: 0.8191 (t0) REVERT: F 259 ARG cc_start: 0.8675 (ttm-80) cc_final: 0.8115 (tpp80) REVERT: F 285 ASN cc_start: 0.8938 (m110) cc_final: 0.8670 (m110) REVERT: F 296 ASN cc_start: 0.8597 (p0) cc_final: 0.8231 (p0) REVERT: F 409 LYS cc_start: 0.8262 (ptpt) cc_final: 0.8013 (ptpt) REVERT: F 461 ILE cc_start: 0.8875 (pt) cc_final: 0.8587 (mt) REVERT: F 491 GLU cc_start: 0.8632 (tp30) cc_final: 0.8353 (tp30) REVERT: G 12 TYR cc_start: 0.7991 (t80) cc_final: 0.7788 (t80) REVERT: G 102 ASN cc_start: 0.8581 (t0) cc_final: 0.7819 (t0) REVERT: G 259 ARG cc_start: 0.8568 (ttm-80) cc_final: 0.8265 (tpp80) REVERT: G 355 ARG cc_start: 0.8920 (ttp-170) cc_final: 0.8534 (ttp-170) REVERT: G 399 GLU cc_start: 0.7767 (mp0) cc_final: 0.7508 (mp0) REVERT: G 441 GLN cc_start: 0.8639 (mt0) cc_final: 0.8349 (mt0) REVERT: G 461 ILE cc_start: 0.8817 (pt) cc_final: 0.8508 (mt) REVERT: G 491 GLU cc_start: 0.8314 (tp30) cc_final: 0.8088 (tp30) REVERT: H 92 HIS cc_start: 0.8457 (p-80) cc_final: 0.8224 (p90) REVERT: H 102 ASN cc_start: 0.8827 (t0) cc_final: 0.8168 (t0) REVERT: H 242 LYS cc_start: 0.8244 (mttp) cc_final: 0.7927 (tppt) REVERT: H 259 ARG cc_start: 0.8859 (tpp80) cc_final: 0.8419 (tpp80) REVERT: H 274 ASP cc_start: 0.8931 (t0) cc_final: 0.8502 (t70) REVERT: H 399 GLU cc_start: 0.7988 (pm20) cc_final: 0.7763 (mp0) REVERT: H 461 ILE cc_start: 0.8794 (pt) cc_final: 0.8486 (mt) outliers start: 96 outliers final: 53 residues processed: 790 average time/residue: 0.1460 time to fit residues: 183.6422 Evaluate side-chains 749 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 692 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR 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 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 259 ARG 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 73 VAL Chi-restraints excluded: chain C residue 271 VAL 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 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 63 THR Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 453 ILE 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 275 SER Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 386 MET 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 275 SER Chi-restraints excluded: chain G residue 281 ILE 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 271 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 282 optimal weight: 0.0970 chunk 142 optimal weight: 0.9980 chunk 177 optimal weight: 0.2980 chunk 141 optimal weight: 10.0000 chunk 144 optimal weight: 0.8980 chunk 261 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 198 optimal weight: 3.9990 chunk 64 optimal weight: 0.1980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** 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 309 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** 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 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.154333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.127900 restraints weight = 32901.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.133023 restraints weight = 17094.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.136506 restraints weight = 10756.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.138841 restraints weight = 7688.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.140530 restraints weight = 6031.083| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23488 Z= 0.124 Angle : 0.657 9.280 31792 Z= 0.323 Chirality : 0.045 0.150 3656 Planarity : 0.004 0.046 4000 Dihedral : 7.974 89.868 3358 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.66 % Allowed : 27.77 % Favored : 67.58 % 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: -1.74 (0.15), residues: 2960 helix: -0.74 (0.15), residues: 1064 sheet: -2.67 (0.23), residues: 384 loop : -0.91 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 355 TYR 0.031 0.002 TYR G 484 PHE 0.015 0.001 PHE F 99 HIS 0.010 0.001 HIS F 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (23480) covalent geometry : angle 0.65664 / 0.32 (31792) hydrogen bonds : bond 0.02830 / 1.84 ( 784) hydrogen bonds : angle 4.85064 / 3.33 ( 2256) Misc. bond : bond 0.00011 / 0.01 ( 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 854 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 743 time to evaluate : 0.862 Fit side-chains REVERT: A 25 ASN cc_start: 0.8675 (m-40) cc_final: 0.8328 (m-40) REVERT: A 92 HIS cc_start: 0.8287 (p-80) cc_final: 0.7969 (p90) REVERT: A 102 ASN cc_start: 0.8638 (t0) cc_final: 0.7906 (t0) REVERT: A 259 ARG cc_start: 0.8868 (tpp80) cc_final: 0.8366 (tpp80) REVERT: A 399 GLU cc_start: 0.7774 (mp0) cc_final: 0.7568 (mp0) REVERT: A 441 GLN cc_start: 0.8623 (mt0) cc_final: 0.8385 (mt0) REVERT: A 483 MET cc_start: 0.9170 (tmm) cc_final: 0.8693 (tmm) REVERT: B 92 HIS cc_start: 0.8511 (p-80) cc_final: 0.8301 (p90) REVERT: B 102 ASN cc_start: 0.8788 (t0) cc_final: 0.8152 (t0) REVERT: B 242 LYS cc_start: 0.8278 (mttp) cc_final: 0.7962 (tppt) REVERT: B 274 ASP cc_start: 0.8890 (t0) cc_final: 0.8607 (t70) REVERT: B 441 GLN cc_start: 0.8624 (mt0) cc_final: 0.8299 (mt0) REVERT: B 461 ILE cc_start: 0.8871 (pt) cc_final: 0.8592 (mt) REVERT: B 483 MET cc_start: 0.9172 (tmm) cc_final: 0.8700 (tmm) REVERT: B 491 GLU cc_start: 0.8613 (tp30) cc_final: 0.8393 (tp30) REVERT: C 92 HIS cc_start: 0.8470 (p-80) cc_final: 0.8163 (p90) REVERT: C 102 ASN cc_start: 0.8714 (t0) cc_final: 0.7959 (t0) REVERT: C 258 TYR cc_start: 0.8505 (t80) cc_final: 0.8275 (t80) REVERT: C 259 ARG cc_start: 0.8815 (tpp80) cc_final: 0.8544 (tpp80) REVERT: C 441 GLN cc_start: 0.8633 (mt0) cc_final: 0.8304 (mt0) REVERT: C 461 ILE cc_start: 0.8899 (pt) cc_final: 0.8630 (mt) REVERT: C 483 MET cc_start: 0.9196 (tmm) cc_final: 0.8664 (tmm) REVERT: D 1 MET cc_start: 0.7605 (tpp) cc_final: 0.7398 (tpp) REVERT: D 12 TYR cc_start: 0.8183 (t80) cc_final: 0.7949 (t80) REVERT: D 59 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7742 (pt) REVERT: D 82 MET cc_start: 0.8753 (mtp) cc_final: 0.8491 (mtm) REVERT: D 102 ASN cc_start: 0.8856 (t0) cc_final: 0.8174 (t0) REVERT: D 274 ASP cc_start: 0.8865 (t0) cc_final: 0.8575 (t70) REVERT: D 399 GLU cc_start: 0.7766 (mp0) cc_final: 0.7431 (mp0) REVERT: D 483 MET cc_start: 0.9177 (tmm) cc_final: 0.8653 (tmm) REVERT: E 12 TYR cc_start: 0.7985 (t80) cc_final: 0.7774 (t80) REVERT: E 43 ASP cc_start: 0.7855 (m-30) cc_final: 0.7600 (m-30) REVERT: E 102 ASN cc_start: 0.8636 (t0) cc_final: 0.7878 (t0) REVERT: E 258 TYR cc_start: 0.8524 (t80) cc_final: 0.8247 (t80) REVERT: E 259 ARG cc_start: 0.8842 (tpp80) cc_final: 0.8308 (tpp80) REVERT: E 441 GLN cc_start: 0.8635 (mt0) cc_final: 0.8417 (mt0) REVERT: E 483 MET cc_start: 0.9200 (tmm) cc_final: 0.8709 (tmm) REVERT: E 491 GLU cc_start: 0.8761 (tp30) cc_final: 0.8452 (tp30) REVERT: F 102 ASN cc_start: 0.8870 (t0) cc_final: 0.8213 (t0) REVERT: F 259 ARG cc_start: 0.8654 (ttm-80) cc_final: 0.8063 (tpp80) REVERT: F 285 ASN cc_start: 0.8921 (m110) cc_final: 0.8696 (m110) REVERT: F 441 GLN cc_start: 0.8578 (mt0) cc_final: 0.8298 (mt0) REVERT: F 461 ILE cc_start: 0.8849 (pt) cc_final: 0.8545 (mt) REVERT: F 491 GLU cc_start: 0.8732 (tp30) cc_final: 0.8397 (tp30) REVERT: G 5 LEU cc_start: 0.8909 (pt) cc_final: 0.8692 (pt) REVERT: G 102 ASN cc_start: 0.8595 (t0) cc_final: 0.7869 (t0) REVERT: G 259 ARG cc_start: 0.8518 (ttm-80) cc_final: 0.8230 (tpp80) REVERT: G 399 GLU cc_start: 0.7764 (mp0) cc_final: 0.7549 (mp0) REVERT: G 441 GLN cc_start: 0.8625 (mt0) cc_final: 0.8376 (mt0) REVERT: G 461 ILE cc_start: 0.8778 (pt) cc_final: 0.8486 (mt) REVERT: G 483 MET cc_start: 0.9136 (tmm) cc_final: 0.8865 (tmm) REVERT: H 102 ASN cc_start: 0.8837 (t0) cc_final: 0.8163 (t0) REVERT: H 242 LYS cc_start: 0.8281 (mttp) cc_final: 0.7910 (tppt) REVERT: H 259 ARG cc_start: 0.8834 (tpp80) cc_final: 0.8388 (tpp80) REVERT: H 274 ASP cc_start: 0.8941 (t0) cc_final: 0.8508 (t70) REVERT: H 448 GLN cc_start: 0.7652 (pt0) cc_final: 0.7410 (pt0) REVERT: H 461 ILE cc_start: 0.8780 (pt) cc_final: 0.8471 (mt) outliers start: 111 outliers final: 58 residues processed: 815 average time/residue: 0.1435 time to fit residues: 185.8890 Evaluate side-chains 765 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 706 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 337 LEU 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 259 ARG 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 271 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 337 LEU 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 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 66 VAL 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 505 SER Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 78 MET 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 73 VAL 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 386 MET 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 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 63 THR Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 275 SER 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: 4.9990 chunk 175 optimal weight: 0.0000 chunk 46 optimal weight: 7.9990 chunk 191 optimal weight: 0.0040 chunk 223 optimal weight: 8.9990 chunk 189 optimal weight: 1.9990 chunk 269 optimal weight: 0.8980 chunk 242 optimal weight: 0.9990 chunk 277 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 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** B 312 ASN C 100 GLN ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN ** 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** ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3698 r_free = 0.3698 target = 0.153614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.127954 restraints weight = 33273.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.132944 restraints weight = 17365.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.136409 restraints weight = 10936.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.138879 restraints weight = 7786.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.140318 restraints weight = 6008.556| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23488 Z= 0.129 Angle : 0.673 11.409 31792 Z= 0.327 Chirality : 0.045 0.178 3656 Planarity : 0.004 0.047 4000 Dihedral : 7.705 89.497 3349 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.69 % Allowed : 29.95 % Favored : 66.36 % 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: -1.61 (0.15), residues: 2960 helix: -0.48 (0.15), residues: 1064 sheet: -3.00 (0.24), residues: 336 loop : -0.94 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 480 TYR 0.027 0.002 TYR B 12 PHE 0.013 0.001 PHE F 99 HIS 0.009 0.001 HIS F 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (23480) covalent geometry : angle 0.67252 / 0.33 (31792) hydrogen bonds : bond 0.02833 / 1.83 ( 784) hydrogen bonds : angle 4.77549 / 3.28 ( 2256) Misc. bond : bond 0.00010 / 0.00 ( 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 841 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 753 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8708 (mtp) cc_final: 0.8399 (mtt) REVERT: A 92 HIS cc_start: 0.8285 (p-80) cc_final: 0.7951 (p90) REVERT: A 102 ASN cc_start: 0.8670 (t0) cc_final: 0.7974 (t0) REVERT: A 259 ARG cc_start: 0.8852 (tpp80) cc_final: 0.8319 (tpp80) REVERT: A 341 ARG cc_start: 0.8985 (ttt180) cc_final: 0.8595 (ttt180) REVERT: A 441 GLN cc_start: 0.8638 (mt0) cc_final: 0.8377 (mt0) REVERT: A 483 MET cc_start: 0.9194 (tmm) cc_final: 0.8723 (tmm) REVERT: B 92 HIS cc_start: 0.8600 (p-80) cc_final: 0.8328 (p90) REVERT: B 102 ASN cc_start: 0.8817 (t0) cc_final: 0.8178 (t0) REVERT: B 242 LYS cc_start: 0.8282 (mttp) cc_final: 0.7951 (tppt) REVERT: B 259 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8533 (ttp-170) REVERT: B 274 ASP cc_start: 0.8919 (t0) cc_final: 0.8633 (t70) REVERT: B 441 GLN cc_start: 0.8663 (mt0) cc_final: 0.8297 (mt0) REVERT: B 461 ILE cc_start: 0.8811 (pt) cc_final: 0.8560 (mt) REVERT: B 483 MET cc_start: 0.9200 (tmm) cc_final: 0.8713 (tmm) REVERT: B 491 GLU cc_start: 0.8746 (tp30) cc_final: 0.8477 (tp30) REVERT: C 92 HIS cc_start: 0.8467 (p-80) cc_final: 0.8144 (p90) REVERT: C 102 ASN cc_start: 0.8731 (t0) cc_final: 0.8004 (t0) REVERT: C 259 ARG cc_start: 0.8821 (tpp80) cc_final: 0.8338 (tpp80) REVERT: C 441 GLN cc_start: 0.8681 (mt0) cc_final: 0.8264 (mt0) REVERT: C 448 GLN cc_start: 0.7706 (pt0) cc_final: 0.7462 (pt0) REVERT: C 465 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8582 (mm-40) REVERT: C 483 MET cc_start: 0.9208 (tmm) cc_final: 0.8702 (tmm) REVERT: D 59 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7758 (pt) REVERT: D 102 ASN cc_start: 0.8875 (t0) cc_final: 0.8201 (t0) REVERT: D 274 ASP cc_start: 0.8902 (t0) cc_final: 0.8619 (t70) REVERT: D 461 ILE cc_start: 0.8914 (pt) cc_final: 0.8493 (mt) REVERT: D 483 MET cc_start: 0.9191 (tmm) cc_final: 0.8679 (tmm) REVERT: D 491 GLU cc_start: 0.8684 (tp30) cc_final: 0.8211 (tp30) REVERT: E 43 ASP cc_start: 0.7811 (m-30) cc_final: 0.7579 (m-30) REVERT: E 78 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7716 (ttm) REVERT: E 102 ASN cc_start: 0.8680 (t0) cc_final: 0.7966 (t0) REVERT: E 258 TYR cc_start: 0.8616 (t80) cc_final: 0.8350 (t80) REVERT: E 259 ARG cc_start: 0.8865 (tpp80) cc_final: 0.8476 (tpp80) REVERT: E 341 ARG cc_start: 0.8960 (ttt180) cc_final: 0.8495 (ttt180) REVERT: E 441 GLN cc_start: 0.8651 (mt0) cc_final: 0.8400 (mt0) REVERT: E 453 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8276 (pt) REVERT: E 491 GLU cc_start: 0.8833 (tp30) cc_final: 0.8617 (tp30) REVERT: F 102 ASN cc_start: 0.8871 (t0) cc_final: 0.8223 (t0) REVERT: F 259 ARG cc_start: 0.8706 (ttm-80) cc_final: 0.8496 (ttm-80) REVERT: F 285 ASN cc_start: 0.8974 (m110) cc_final: 0.8745 (m110) REVERT: F 341 ARG cc_start: 0.9120 (ttt180) cc_final: 0.8909 (ttt180) REVERT: F 441 GLN cc_start: 0.8614 (mt0) cc_final: 0.8322 (mt0) REVERT: F 461 ILE cc_start: 0.8817 (pt) cc_final: 0.8528 (mt) REVERT: F 491 GLU cc_start: 0.8735 (tp30) cc_final: 0.8460 (tp30) REVERT: G 102 ASN cc_start: 0.8619 (t0) cc_final: 0.7881 (t0) REVERT: G 259 ARG cc_start: 0.8525 (ttm-80) cc_final: 0.8230 (tpp80) REVERT: G 356 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7181 (mpp80) REVERT: G 441 GLN cc_start: 0.8669 (mt0) cc_final: 0.8415 (mt0) REVERT: G 461 ILE cc_start: 0.8758 (pt) cc_final: 0.8480 (mt) REVERT: H 102 ASN cc_start: 0.8868 (t0) cc_final: 0.8219 (t0) REVERT: H 242 LYS cc_start: 0.8303 (mttp) cc_final: 0.7895 (tppt) REVERT: H 259 ARG cc_start: 0.8836 (tpp80) cc_final: 0.8382 (tpp80) REVERT: H 274 ASP cc_start: 0.8956 (t0) cc_final: 0.8539 (t70) REVERT: H 448 GLN cc_start: 0.7651 (pt0) cc_final: 0.7390 (pt0) REVERT: H 461 ILE cc_start: 0.8697 (pt) cc_final: 0.8464 (mt) outliers start: 88 outliers final: 54 residues processed: 807 average time/residue: 0.1490 time to fit residues: 190.4317 Evaluate side-chains 771 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 711 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 63 THR 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 457 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain C residue 469 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 66 VAL 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 63 THR Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 18 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 356 ARG Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 386 MET 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 260 LEU Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 356 ARG Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 437 ILE 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 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: 3.9990 chunk 233 optimal weight: 10.0000 chunk 104 optimal weight: 0.0870 chunk 63 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 295 optimal weight: 3.9990 chunk 281 optimal weight: 0.3980 chunk 252 optimal weight: 0.9990 chunk 133 optimal weight: 0.3980 chunk 103 optimal weight: 3.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN A 243 GLN ** 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** B 312 ASN ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** 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 G 309 GLN G 312 ASN H 100 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.154138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.128566 restraints weight = 33111.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.133550 restraints weight = 17364.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.136996 restraints weight = 10961.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.139362 restraints weight = 7814.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.141103 restraints weight = 6072.732| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23488 Z= 0.129 Angle : 0.682 8.634 31792 Z= 0.332 Chirality : 0.045 0.160 3656 Planarity : 0.004 0.055 4000 Dihedral : 7.557 89.989 3340 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.36 % Allowed : 31.25 % Favored : 65.39 % 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: -1.35 (0.15), residues: 2960 helix: -0.24 (0.16), residues: 1064 sheet: -3.08 (0.28), residues: 256 loop : -0.91 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 355 TYR 0.025 0.002 TYR D 4 PHE 0.013 0.001 PHE H 44 HIS 0.009 0.001 HIS F 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (23480) covalent geometry : angle 0.68201 / 0.33 (31792) hydrogen bonds : bond 0.02773 / 1.79 ( 784) hydrogen bonds : angle 4.73953 / 3.25 ( 2256) Misc. bond : bond 0.00012 / 0.01 ( 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 824 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 744 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 92 HIS cc_start: 0.8428 (p-80) cc_final: 0.8100 (p90) REVERT: A 102 ASN cc_start: 0.8713 (t0) cc_final: 0.8002 (t0) REVERT: A 259 ARG cc_start: 0.8793 (tpp80) cc_final: 0.8468 (tpp80) REVERT: A 341 ARG cc_start: 0.8902 (ttt180) cc_final: 0.8429 (ttt180) REVERT: A 438 LYS cc_start: 0.7425 (mmtt) cc_final: 0.7203 (mmtm) REVERT: A 441 GLN cc_start: 0.8637 (mt0) cc_final: 0.8375 (mt0) REVERT: B 92 HIS cc_start: 0.8585 (p-80) cc_final: 0.8287 (p90) REVERT: B 102 ASN cc_start: 0.8797 (t0) cc_final: 0.8128 (t0) REVERT: B 242 LYS cc_start: 0.8288 (mttp) cc_final: 0.7959 (tppt) REVERT: B 274 ASP cc_start: 0.8860 (t0) cc_final: 0.8598 (t70) REVERT: B 441 GLN cc_start: 0.8664 (mt0) cc_final: 0.8322 (mt0) REVERT: B 461 ILE cc_start: 0.8792 (pt) cc_final: 0.8520 (mt) REVERT: C 92 HIS cc_start: 0.8493 (p-80) cc_final: 0.8179 (p90) REVERT: C 102 ASN cc_start: 0.8717 (t0) cc_final: 0.7974 (t0) REVERT: C 259 ARG cc_start: 0.8772 (tpp80) cc_final: 0.8455 (tpp80) REVERT: C 327 SER cc_start: 0.8503 (p) cc_final: 0.8183 (p) REVERT: C 409 LYS cc_start: 0.8055 (ptpt) cc_final: 0.7792 (pttt) REVERT: C 441 GLN cc_start: 0.8691 (mt0) cc_final: 0.8314 (mt0) REVERT: C 491 GLU cc_start: 0.8684 (tp30) cc_final: 0.8203 (tp30) REVERT: D 59 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7595 (pt) REVERT: D 102 ASN cc_start: 0.8866 (t0) cc_final: 0.8197 (t0) REVERT: D 274 ASP cc_start: 0.8811 (t0) cc_final: 0.8539 (t70) REVERT: D 341 ARG cc_start: 0.8971 (ttt180) cc_final: 0.8658 (ttt180) REVERT: D 448 GLN cc_start: 0.7562 (pt0) cc_final: 0.7328 (pt0) REVERT: D 461 ILE cc_start: 0.8854 (pt) cc_final: 0.8443 (mt) REVERT: D 483 MET cc_start: 0.9218 (tmm) cc_final: 0.8716 (tmm) REVERT: D 491 GLU cc_start: 0.8695 (tp30) cc_final: 0.8142 (tp30) REVERT: E 43 ASP cc_start: 0.7832 (m-30) cc_final: 0.7578 (m-30) REVERT: E 102 ASN cc_start: 0.8672 (t0) cc_final: 0.7948 (t0) REVERT: E 258 TYR cc_start: 0.8606 (t80) cc_final: 0.8303 (t80) REVERT: E 259 ARG cc_start: 0.8839 (tpp80) cc_final: 0.8413 (tpp80) REVERT: E 341 ARG cc_start: 0.8895 (ttt180) cc_final: 0.8459 (ttt180) REVERT: E 441 GLN cc_start: 0.8645 (mt0) cc_final: 0.8421 (mt0) REVERT: E 453 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8233 (pt) REVERT: E 491 GLU cc_start: 0.8861 (tp30) cc_final: 0.8458 (tp30) REVERT: F 102 ASN cc_start: 0.8879 (t0) cc_final: 0.8284 (t0) REVERT: F 285 ASN cc_start: 0.9000 (m110) cc_final: 0.8748 (m110) REVERT: F 409 LYS cc_start: 0.8106 (ptpt) cc_final: 0.7742 (pttt) REVERT: F 441 GLN cc_start: 0.8633 (mt0) cc_final: 0.8342 (mt0) REVERT: F 461 ILE cc_start: 0.8772 (pt) cc_final: 0.8483 (mt) REVERT: F 491 GLU cc_start: 0.8716 (tp30) cc_final: 0.8376 (tp30) REVERT: G 102 ASN cc_start: 0.8663 (t0) cc_final: 0.7950 (t0) REVERT: G 259 ARG cc_start: 0.8517 (ttm-80) cc_final: 0.8268 (tpp80) REVERT: G 341 ARG cc_start: 0.8894 (ttt180) cc_final: 0.8451 (ttt180) REVERT: G 441 GLN cc_start: 0.8669 (mt0) cc_final: 0.8410 (mt0) REVERT: G 461 ILE cc_start: 0.8735 (pt) cc_final: 0.8450 (mt) REVERT: H 102 ASN cc_start: 0.8836 (t0) cc_final: 0.8193 (t0) REVERT: H 242 LYS cc_start: 0.8315 (mttp) cc_final: 0.7891 (tppt) REVERT: H 259 ARG cc_start: 0.8811 (tpp80) cc_final: 0.8355 (tpp80) REVERT: H 274 ASP cc_start: 0.8963 (t0) cc_final: 0.8574 (t70) REVERT: H 448 GLN cc_start: 0.7640 (pt0) cc_final: 0.7391 (pt0) REVERT: H 461 ILE cc_start: 0.8697 (pt) cc_final: 0.8486 (mt) REVERT: H 491 GLU cc_start: 0.8706 (tp30) cc_final: 0.8285 (tp30) outliers start: 80 outliers final: 57 residues processed: 790 average time/residue: 0.1581 time to fit residues: 196.7429 Evaluate side-chains 780 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 721 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 63 THR 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 503 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 259 ARG 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 C residue 18 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 73 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 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 500 GLU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 18 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 356 ARG Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain G residue 18 LEU 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 263 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 281 ILE 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 275 SER Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 453 ILE 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: 0.9980 chunk 227 optimal weight: 6.9990 chunk 225 optimal weight: 0.0370 chunk 287 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 261 optimal weight: 4.9990 chunk 146 optimal weight: 0.0170 chunk 247 optimal weight: 0.5980 chunk 292 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN ** 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** B 312 ASN ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 ASN H 303 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.154988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.129790 restraints weight = 32396.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.134782 restraints weight = 17054.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.138136 restraints weight = 10652.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.140617 restraints weight = 7511.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.142147 restraints weight = 5761.556| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4017 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= 0.128 Angle : 0.693 9.773 31792 Z= 0.336 Chirality : 0.045 0.161 3656 Planarity : 0.004 0.046 4000 Dihedral : 7.427 89.061 3334 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.36 % Allowed : 31.71 % Favored : 64.93 % 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: -1.27 (0.15), residues: 2960 helix: -0.12 (0.16), residues: 1072 sheet: -2.91 (0.28), residues: 256 loop : -0.92 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 355 TYR 0.024 0.002 TYR D 12 PHE 0.013 0.001 PHE D 44 HIS 0.006 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (23480) covalent geometry : angle 0.69319 / 0.34 (31792) hydrogen bonds : bond 0.02757 / 1.76 ( 784) hydrogen bonds : angle 4.68828 / 3.21 ( 2256) Misc. bond : bond 0.00010 / 0.00 ( 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 836 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 756 time to evaluate : 0.873 Fit side-chains REVERT: A 5 LEU cc_start: 0.8884 (pt) cc_final: 0.8516 (pt) REVERT: A 92 HIS cc_start: 0.8486 (p-80) cc_final: 0.8121 (p90) REVERT: A 102 ASN cc_start: 0.8701 (t0) cc_final: 0.7997 (t0) REVERT: A 259 ARG cc_start: 0.8802 (tpp80) cc_final: 0.8280 (tpp80) REVERT: A 341 ARG cc_start: 0.8910 (ttt180) cc_final: 0.8489 (ttt180) REVERT: A 355 ARG cc_start: 0.8524 (ttp-170) cc_final: 0.8320 (ttp-170) REVERT: A 441 GLN cc_start: 0.8627 (mt0) cc_final: 0.8361 (mt0) REVERT: A 483 MET cc_start: 0.9188 (tmm) cc_final: 0.8667 (tmm) REVERT: B 5 LEU cc_start: 0.8960 (pt) cc_final: 0.8644 (pt) REVERT: B 92 HIS cc_start: 0.8617 (p-80) cc_final: 0.8286 (p90) REVERT: B 102 ASN cc_start: 0.8851 (t0) cc_final: 0.8203 (t0) REVERT: B 242 LYS cc_start: 0.8339 (mttp) cc_final: 0.7952 (tppt) REVERT: B 274 ASP cc_start: 0.8829 (t0) cc_final: 0.8558 (t70) REVERT: B 441 GLN cc_start: 0.8687 (mt0) cc_final: 0.8351 (mt0) REVERT: B 461 ILE cc_start: 0.8759 (pt) cc_final: 0.8496 (mt) REVERT: B 491 GLU cc_start: 0.8874 (tp30) cc_final: 0.8625 (tp30) REVERT: C 75 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7258 (mm-30) REVERT: C 102 ASN cc_start: 0.8732 (t0) cc_final: 0.8016 (t0) REVERT: C 259 ARG cc_start: 0.8749 (tpp80) cc_final: 0.8424 (tpp80) REVERT: C 327 SER cc_start: 0.8476 (p) cc_final: 0.8161 (p) REVERT: C 409 LYS cc_start: 0.8132 (ptpt) cc_final: 0.7552 (pttt) REVERT: C 441 GLN cc_start: 0.8687 (mt0) cc_final: 0.8349 (mt0) REVERT: C 465 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8555 (mm110) REVERT: C 483 MET cc_start: 0.9175 (tmm) cc_final: 0.8725 (tmm) REVERT: C 491 GLU cc_start: 0.8714 (tp30) cc_final: 0.8177 (tp30) REVERT: D 59 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7421 (pt) REVERT: D 102 ASN cc_start: 0.8889 (t0) cc_final: 0.8238 (t0) REVERT: D 274 ASP cc_start: 0.8788 (t0) cc_final: 0.8533 (t70) REVERT: D 341 ARG cc_start: 0.8993 (ttt180) cc_final: 0.8664 (ttt180) REVERT: D 448 GLN cc_start: 0.7574 (pt0) cc_final: 0.7338 (pt0) REVERT: D 461 ILE cc_start: 0.8881 (pt) cc_final: 0.8509 (mt) REVERT: E 43 ASP cc_start: 0.7884 (m-30) cc_final: 0.7630 (m-30) REVERT: E 78 MET cc_start: 0.8483 (tpp) cc_final: 0.8122 (tpp) REVERT: E 99 PHE cc_start: 0.9095 (t80) cc_final: 0.8836 (t80) REVERT: E 102 ASN cc_start: 0.8673 (t0) cc_final: 0.7991 (t0) REVERT: E 258 TYR cc_start: 0.8651 (t80) cc_final: 0.8375 (t80) REVERT: E 259 ARG cc_start: 0.8838 (tpp80) cc_final: 0.8242 (tpp80) REVERT: E 341 ARG cc_start: 0.8892 (ttt180) cc_final: 0.8485 (ttt180) REVERT: E 441 GLN cc_start: 0.8645 (mt0) cc_final: 0.8426 (mt0) REVERT: E 453 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8159 (pt) REVERT: E 491 GLU cc_start: 0.8910 (tp30) cc_final: 0.8450 (tp30) REVERT: F 92 HIS cc_start: 0.8255 (p-80) cc_final: 0.8052 (p90) REVERT: F 102 ASN cc_start: 0.8944 (t0) cc_final: 0.8415 (t0) REVERT: F 285 ASN cc_start: 0.9082 (m110) cc_final: 0.8826 (m110) REVERT: F 312 ASN cc_start: 0.9207 (m-40) cc_final: 0.8556 (m-40) REVERT: F 386 MET cc_start: 0.8865 (ptp) cc_final: 0.8619 (ptp) REVERT: F 409 LYS cc_start: 0.8024 (ptpt) cc_final: 0.7673 (pttt) REVERT: F 441 GLN cc_start: 0.8640 (mt0) cc_final: 0.8338 (mt0) REVERT: F 461 ILE cc_start: 0.8759 (pt) cc_final: 0.8495 (mt) REVERT: F 491 GLU cc_start: 0.8758 (tp30) cc_final: 0.8438 (tp30) REVERT: G 102 ASN cc_start: 0.8678 (t0) cc_final: 0.7953 (t0) REVERT: G 259 ARG cc_start: 0.8555 (ttm-80) cc_final: 0.8191 (tpp80) REVERT: G 341 ARG cc_start: 0.8882 (ttt180) cc_final: 0.8470 (ttt180) REVERT: G 441 GLN cc_start: 0.8699 (mt0) cc_final: 0.8432 (mt0) REVERT: G 461 ILE cc_start: 0.8715 (pt) cc_final: 0.8387 (mt) REVERT: G 465 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8484 (mm-40) REVERT: H 102 ASN cc_start: 0.8870 (t0) cc_final: 0.8247 (t0) REVERT: H 242 LYS cc_start: 0.8306 (mttp) cc_final: 0.7871 (tppt) REVERT: H 259 ARG cc_start: 0.8798 (tpp80) cc_final: 0.8314 (tpp80) REVERT: H 274 ASP cc_start: 0.8973 (t0) cc_final: 0.8561 (t70) REVERT: H 441 GLN cc_start: 0.8585 (mt0) cc_final: 0.8273 (mt0) REVERT: H 448 GLN cc_start: 0.7600 (pt0) cc_final: 0.7360 (pt0) REVERT: H 461 ILE cc_start: 0.8668 (pt) cc_final: 0.8397 (mt) REVERT: H 491 GLU cc_start: 0.8744 (tp30) cc_final: 0.8258 (tp30) outliers start: 80 outliers final: 54 residues processed: 806 average time/residue: 0.1508 time to fit residues: 192.2354 Evaluate side-chains 776 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 718 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 18 LEU 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 469 GLN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 73 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 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 299 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 63 THR 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 388 SER Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain G residue 18 LEU 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 263 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 465 GLN 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 275 SER Chi-restraints excluded: chain H residue 382 SER 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: 7.9990 chunk 192 optimal weight: 5.9990 chunk 239 optimal weight: 1.9990 chunk 262 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 253 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 225 optimal weight: 0.7980 chunk 200 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** B 312 ASN B 368 GLN ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 ASN H 368 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.150254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.124989 restraints weight = 32992.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.129889 restraints weight = 17292.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.133244 restraints weight = 10848.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.135499 restraints weight = 7675.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.137046 restraints weight = 5951.747| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23488 Z= 0.161 Angle : 0.718 9.414 31792 Z= 0.352 Chirality : 0.046 0.162 3656 Planarity : 0.004 0.048 4000 Dihedral : 7.462 89.604 3334 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.27 % Allowed : 32.59 % Favored : 64.14 % 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: -1.33 (0.15), residues: 2960 helix: -0.22 (0.16), residues: 1120 sheet: -2.81 (0.29), residues: 256 loop : -0.96 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 480 TYR 0.035 0.002 TYR A 484 PHE 0.017 0.001 PHE F 44 HIS 0.008 0.001 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (23480) covalent geometry : angle 0.71828 / 0.35 (31792) hydrogen bonds : bond 0.02957 / 1.88 ( 784) hydrogen bonds : angle 4.69150 / 3.22 ( 2256) Misc. bond : bond 0.00075 / 0.04 ( 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 814 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 736 time to evaluate : 0.842 Fit side-chains REVERT: A 5 LEU cc_start: 0.8908 (pt) cc_final: 0.8565 (pt) REVERT: A 92 HIS cc_start: 0.8534 (p-80) cc_final: 0.8153 (p90) REVERT: A 102 ASN cc_start: 0.8723 (t0) cc_final: 0.8009 (t0) REVERT: A 257 LYS cc_start: 0.9229 (mttm) cc_final: 0.9017 (mttm) REVERT: A 259 ARG cc_start: 0.8821 (tpp80) cc_final: 0.8312 (tpp80) REVERT: A 441 GLN cc_start: 0.8685 (mt0) cc_final: 0.8380 (mt0) REVERT: A 483 MET cc_start: 0.9134 (tmm) cc_final: 0.8863 (tmm) REVERT: B 5 LEU cc_start: 0.9067 (pt) cc_final: 0.8621 (pt) REVERT: B 92 HIS cc_start: 0.8738 (p-80) cc_final: 0.8354 (p90) REVERT: B 102 ASN cc_start: 0.8865 (t0) cc_final: 0.8216 (t0) REVERT: B 242 LYS cc_start: 0.8345 (mttp) cc_final: 0.7972 (tppt) REVERT: B 259 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8521 (tpp80) REVERT: B 274 ASP cc_start: 0.8921 (t0) cc_final: 0.8680 (t70) REVERT: B 441 GLN cc_start: 0.8709 (mt0) cc_final: 0.8326 (mt0) REVERT: B 461 ILE cc_start: 0.8782 (pt) cc_final: 0.8491 (mt) REVERT: B 491 GLU cc_start: 0.8884 (tp30) cc_final: 0.8635 (tp30) REVERT: C 102 ASN cc_start: 0.8915 (t0) cc_final: 0.8320 (t0) REVERT: C 103 GLU cc_start: 0.8731 (tp30) cc_final: 0.8318 (tp30) REVERT: C 259 ARG cc_start: 0.8770 (tpp80) cc_final: 0.8457 (tpp80) REVERT: C 327 SER cc_start: 0.8635 (p) cc_final: 0.8316 (p) REVERT: C 441 GLN cc_start: 0.8726 (mt0) cc_final: 0.8290 (mt0) REVERT: C 465 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8558 (mm-40) REVERT: C 483 MET cc_start: 0.9134 (tmm) cc_final: 0.8933 (tmm) REVERT: C 491 GLU cc_start: 0.8722 (tp30) cc_final: 0.8135 (tp30) REVERT: D 59 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7598 (pt) REVERT: D 102 ASN cc_start: 0.8935 (t0) cc_final: 0.8324 (t0) REVERT: D 274 ASP cc_start: 0.8938 (t0) cc_final: 0.8689 (t70) REVERT: D 341 ARG cc_start: 0.9009 (ttt180) cc_final: 0.8637 (ttt180) REVERT: D 441 GLN cc_start: 0.8676 (mt0) cc_final: 0.8319 (mt0) REVERT: D 448 GLN cc_start: 0.7591 (pt0) cc_final: 0.7378 (pt0) REVERT: D 461 ILE cc_start: 0.8842 (pt) cc_final: 0.8435 (mt) REVERT: E 43 ASP cc_start: 0.7948 (m-30) cc_final: 0.7669 (m-30) REVERT: E 78 MET cc_start: 0.8520 (tpp) cc_final: 0.8154 (tpp) REVERT: E 102 ASN cc_start: 0.8697 (t0) cc_final: 0.8016 (t0) REVERT: E 259 ARG cc_start: 0.8890 (tpp80) cc_final: 0.8446 (tpp80) REVERT: E 341 ARG cc_start: 0.8934 (ttt180) cc_final: 0.8427 (ttt180) REVERT: E 441 GLN cc_start: 0.8669 (mt0) cc_final: 0.8323 (mt0) REVERT: E 491 GLU cc_start: 0.8946 (tp30) cc_final: 0.8484 (tp30) REVERT: F 5 LEU cc_start: 0.9107 (pt) cc_final: 0.8828 (pt) REVERT: F 92 HIS cc_start: 0.8409 (p-80) cc_final: 0.8161 (p90) REVERT: F 102 ASN cc_start: 0.8935 (t0) cc_final: 0.8351 (t0) REVERT: F 259 ARG cc_start: 0.8746 (ttm-80) cc_final: 0.8403 (tpp80) REVERT: F 285 ASN cc_start: 0.9126 (m110) cc_final: 0.8741 (m-40) REVERT: F 312 ASN cc_start: 0.9250 (m-40) cc_final: 0.8576 (m-40) REVERT: F 386 MET cc_start: 0.8961 (ptp) cc_final: 0.8662 (ptt) REVERT: F 441 GLN cc_start: 0.8672 (mt0) cc_final: 0.8294 (mt0) REVERT: F 461 ILE cc_start: 0.8762 (pt) cc_final: 0.8541 (mt) REVERT: F 491 GLU cc_start: 0.8803 (tp30) cc_final: 0.8493 (tp30) REVERT: G 102 ASN cc_start: 0.8698 (t0) cc_final: 0.7987 (t0) REVERT: G 259 ARG cc_start: 0.8610 (ttm-80) cc_final: 0.8245 (tpp80) REVERT: G 341 ARG cc_start: 0.8910 (ttt180) cc_final: 0.8477 (ttt180) REVERT: G 441 GLN cc_start: 0.8696 (mt0) cc_final: 0.8347 (mt0) REVERT: G 461 ILE cc_start: 0.8745 (pt) cc_final: 0.8399 (mt) REVERT: G 465 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8582 (mm-40) REVERT: H 99 PHE cc_start: 0.9175 (t80) cc_final: 0.8924 (t80) REVERT: H 102 ASN cc_start: 0.8871 (t0) cc_final: 0.8237 (t0) REVERT: H 242 LYS cc_start: 0.8344 (mttp) cc_final: 0.7912 (tppt) REVERT: H 259 ARG cc_start: 0.8848 (tpp80) cc_final: 0.8357 (tpp80) REVERT: H 274 ASP cc_start: 0.9003 (t0) cc_final: 0.8634 (t70) REVERT: H 356 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7717 (mpp80) REVERT: H 441 GLN cc_start: 0.8749 (mt0) cc_final: 0.8283 (mt0) REVERT: H 448 GLN cc_start: 0.7627 (pt0) cc_final: 0.7404 (pt0) REVERT: H 461 ILE cc_start: 0.8722 (pt) cc_final: 0.8422 (mt) REVERT: H 491 GLU cc_start: 0.8727 (tp30) cc_final: 0.8224 (tp30) outliers start: 78 outliers final: 55 residues processed: 791 average time/residue: 0.1462 time to fit residues: 182.7311 Evaluate side-chains 770 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 710 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 25 ASN 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 503 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 73 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 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 103 GLU Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 103 GLU 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 18 LEU Chi-restraints excluded: chain F residue 63 THR 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 382 SER Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 457 VAL Chi-restraints excluded: chain G residue 465 GLN 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 275 SER Chi-restraints excluded: chain H residue 356 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 168 optimal weight: 5.9990 chunk 218 optimal weight: 0.7980 chunk 54 optimal weight: 0.0870 chunk 283 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 141 optimal weight: 0.0980 chunk 181 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 178 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 GLN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 ASN H 465 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.153339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.128405 restraints weight = 32762.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.133370 restraints weight = 17163.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.136798 restraints weight = 10677.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.139029 restraints weight = 7483.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.140757 restraints weight = 5777.685| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23488 Z= 0.134 Angle : 0.716 9.590 31792 Z= 0.349 Chirality : 0.045 0.178 3656 Planarity : 0.004 0.047 4000 Dihedral : 7.454 89.826 3334 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.85 % Allowed : 33.18 % Favored : 63.97 % 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: -1.14 (0.15), residues: 2960 helix: -0.01 (0.16), residues: 1072 sheet: -2.74 (0.29), residues: 256 loop : -0.86 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 480 TYR 0.028 0.002 TYR D 289 PHE 0.015 0.001 PHE F 44 HIS 0.008 0.001 HIS E 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 (23480) covalent geometry : angle 0.71604 / 0.35 (31792) hydrogen bonds : bond 0.02832 / 1.79 ( 784) hydrogen bonds : angle 4.70542 / 3.23 ( 2256) Misc. bond : bond 0.00019 / 0.01 ( 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 799 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 731 time to evaluate : 0.863 Fit side-chains REVERT: A 92 HIS cc_start: 0.8529 (p-80) cc_final: 0.8115 (p90) REVERT: A 102 ASN cc_start: 0.8771 (t0) cc_final: 0.8152 (t0) REVERT: A 259 ARG cc_start: 0.8805 (tpp80) cc_final: 0.8277 (tpp80) REVERT: A 441 GLN cc_start: 0.8667 (mt0) cc_final: 0.8388 (mt0) REVERT: A 483 MET cc_start: 0.9118 (tmm) cc_final: 0.8731 (tmm) REVERT: B 92 HIS cc_start: 0.8682 (p-80) cc_final: 0.8319 (p90) REVERT: B 102 ASN cc_start: 0.8877 (t0) cc_final: 0.8229 (t0) REVERT: B 242 LYS cc_start: 0.8322 (mttp) cc_final: 0.7952 (tppt) REVERT: B 259 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8405 (tpp80) REVERT: B 274 ASP cc_start: 0.8887 (t0) cc_final: 0.8643 (t70) REVERT: B 441 GLN cc_start: 0.8715 (mt0) cc_final: 0.8383 (mt0) REVERT: B 461 ILE cc_start: 0.8756 (pt) cc_final: 0.8493 (mt) REVERT: B 491 GLU cc_start: 0.8878 (tp30) cc_final: 0.8614 (tp30) REVERT: C 50 ASP cc_start: 0.8206 (t0) cc_final: 0.8006 (t0) REVERT: C 102 ASN cc_start: 0.8915 (t0) cc_final: 0.8317 (t0) REVERT: C 103 GLU cc_start: 0.8713 (tp30) cc_final: 0.8367 (tp30) REVERT: C 257 LYS cc_start: 0.9291 (mttm) cc_final: 0.8994 (mmtp) REVERT: C 259 ARG cc_start: 0.8727 (tpp80) cc_final: 0.8410 (tpp80) REVERT: C 327 SER cc_start: 0.8614 (p) cc_final: 0.8304 (p) REVERT: C 438 LYS cc_start: 0.7402 (mmtt) cc_final: 0.7180 (mmtm) REVERT: C 441 GLN cc_start: 0.8706 (mt0) cc_final: 0.8375 (mt0) REVERT: C 465 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8560 (mm110) REVERT: C 483 MET cc_start: 0.9129 (tmm) cc_final: 0.8866 (tmm) REVERT: C 491 GLU cc_start: 0.8712 (tp30) cc_final: 0.8109 (tp30) REVERT: D 59 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7508 (pt) REVERT: D 102 ASN cc_start: 0.8922 (t0) cc_final: 0.8371 (t0) REVERT: D 274 ASP cc_start: 0.8853 (t0) cc_final: 0.8615 (t70) REVERT: D 341 ARG cc_start: 0.9012 (ttt180) cc_final: 0.8673 (ttt180) REVERT: D 441 GLN cc_start: 0.8680 (mt0) cc_final: 0.8307 (mt0) REVERT: D 448 GLN cc_start: 0.7589 (pt0) cc_final: 0.7367 (pt0) REVERT: D 461 ILE cc_start: 0.8779 (pt) cc_final: 0.8316 (mt) REVERT: D 465 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8223 (mm-40) REVERT: E 43 ASP cc_start: 0.8035 (m-30) cc_final: 0.7745 (m-30) REVERT: E 78 MET cc_start: 0.8433 (tpp) cc_final: 0.8137 (tpp) REVERT: E 102 ASN cc_start: 0.8710 (t0) cc_final: 0.8034 (t0) REVERT: E 259 ARG cc_start: 0.8836 (tpp80) cc_final: 0.8435 (tpp80) REVERT: E 341 ARG cc_start: 0.8943 (ttt180) cc_final: 0.8530 (ttt180) REVERT: E 441 GLN cc_start: 0.8661 (mt0) cc_final: 0.8418 (mt0) REVERT: E 491 GLU cc_start: 0.8929 (tp30) cc_final: 0.8469 (tp30) REVERT: F 92 HIS cc_start: 0.8388 (p-80) cc_final: 0.8134 (p90) REVERT: F 102 ASN cc_start: 0.8985 (t0) cc_final: 0.8455 (t0) REVERT: F 285 ASN cc_start: 0.9141 (m110) cc_final: 0.8801 (m-40) REVERT: F 386 MET cc_start: 0.8864 (ptp) cc_final: 0.8580 (ptt) REVERT: F 441 GLN cc_start: 0.8671 (mt0) cc_final: 0.8387 (mt0) REVERT: F 461 ILE cc_start: 0.8772 (pt) cc_final: 0.8487 (mt) REVERT: F 491 GLU cc_start: 0.8779 (tp30) cc_final: 0.8418 (tp30) REVERT: G 102 ASN cc_start: 0.8685 (t0) cc_final: 0.7992 (t0) REVERT: G 259 ARG cc_start: 0.8572 (ttm-80) cc_final: 0.8200 (tpp80) REVERT: G 341 ARG cc_start: 0.8926 (ttt180) cc_final: 0.8508 (ttt180) REVERT: G 441 GLN cc_start: 0.8678 (mt0) cc_final: 0.8330 (mt0) REVERT: G 465 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8596 (mm-40) REVERT: H 99 PHE cc_start: 0.9162 (t80) cc_final: 0.8959 (t80) REVERT: H 102 ASN cc_start: 0.8877 (t0) cc_final: 0.8264 (t0) REVERT: H 242 LYS cc_start: 0.8321 (mttp) cc_final: 0.7853 (tppt) REVERT: H 259 ARG cc_start: 0.8778 (tpp80) cc_final: 0.8292 (tpp80) REVERT: H 274 ASP cc_start: 0.8979 (t0) cc_final: 0.8592 (t70) REVERT: H 441 GLN cc_start: 0.8673 (mt0) cc_final: 0.8214 (mt0) REVERT: H 461 ILE cc_start: 0.8656 (pt) cc_final: 0.8281 (mt) REVERT: H 465 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8363 (mm-40) REVERT: H 491 GLU cc_start: 0.8745 (tp30) cc_final: 0.8157 (tp30) outliers start: 68 outliers final: 52 residues processed: 772 average time/residue: 0.1487 time to fit residues: 182.0020 Evaluate side-chains 757 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 699 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU 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 503 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 63 THR 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 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 299 VAL Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 103 GLU 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 6 ILE Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 63 THR 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 503 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 457 VAL Chi-restraints excluded: chain G residue 465 GLN Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain H residue 18 LEU 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 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: 4.9990 chunk 80 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 256 optimal weight: 0.9990 chunk 179 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 164 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 170 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.152716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.127971 restraints weight = 32639.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.132941 restraints weight = 17018.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.136248 restraints weight = 10571.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.138634 restraints weight = 7425.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.140149 restraints weight = 5689.533| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.199 23488 Z= 0.206 Angle : 0.938 59.187 31792 Z= 0.511 Chirality : 0.046 0.303 3656 Planarity : 0.006 0.194 4000 Dihedral : 7.489 89.847 3334 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.83 % Favored : 95.14 % Rotamer: Outliers : 3.02 % Allowed : 33.68 % Favored : 63.30 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.18 (0.15), residues: 2960 helix: -0.08 (0.16), residues: 1072 sheet: -2.74 (0.29), residues: 256 loop : -0.86 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 356 TYR 0.086 0.003 TYR H 12 PHE 0.021 0.001 PHE A 282 HIS 0.008 0.001 HIS E 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.21 (23480) covalent geometry : angle 0.93848 / 0.51 (31792) hydrogen bonds : bond 0.02862 / 1.82 ( 784) hydrogen bonds : angle 4.72158 / 3.24 ( 2256) Misc. bond : bond 0.00032 / 0.02 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4164.31 seconds wall clock time: 72 minutes 55.11 seconds (4375.11 seconds total)