Starting phenix.real_space_refine on Sat Jul 4 07:56:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zp9_60330/07_2026/8zp9_60330.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zp9_60330/07_2026/8zp9_60330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zp9_60330/07_2026/8zp9_60330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zp9_60330/07_2026/8zp9_60330.map" model { file = "/net/cci-nas-00/data/ceres_data/8zp9_60330/07_2026/8zp9_60330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zp9_60330/07_2026/8zp9_60330.cif" } resolution = 2.8 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= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 429 atoms to isotropic. 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 73 5.49 5 S 74 5.16 5 C 11929 2.51 5 N 3392 2.21 5 O 3829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19297 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 879 Classifications: {'RNA': 41} Modifications used: {'5*END': 1, 'rna2p_pur': 13, 'rna2p_pyr': 7, 'rna3p_pur': 11, 'rna3p_pyr': 10} Link IDs: {'rna2p': 19, 'rna3p': 21} Chain: "F" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2819 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 13, 'TRANS': 354} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2878 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 13, 'TRANS': 361} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "I" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2854 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 13, 'TRANS': 359} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "J" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2845 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 360} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "K" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2646 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 331} Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "G" Number of atoms: 1927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1927 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain breaks: 3 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1780 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 206} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 669 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Time building chain proxies: 4.31, per 1000 atoms: 0.22 Number of scatterers: 19297 At special positions: 0 Unit cell: (114.736, 130.088, 171.296, 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 74 16.00 P 73 15.00 O 3829 8.00 N 3392 7.00 C 11929 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=0, symmetry=0 Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 999.9 milliseconds 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4320 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 23 sheets defined 37.2% alpha, 20.4% beta 12 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'F' and resid 38 through 48 Processing helix chain 'F' and resid 49 through 53 removed outlier: 3.653A pdb=" N LYS F 53 " --> pdb=" O ASN F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 71 removed outlier: 3.750A pdb=" N GLU F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 89 Processing helix chain 'F' and resid 105 through 116 Processing helix chain 'F' and resid 122 through 136 Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 223 through 231 Processing helix chain 'F' and resid 233 through 251 Processing helix chain 'F' and resid 279 through 285 removed outlier: 4.538A pdb=" N ASN F 282 " --> pdb=" O SER F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 313 Processing helix chain 'F' and resid 329 through 332 Processing helix chain 'F' and resid 349 through 362 Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 49 through 53 Processing helix chain 'H' and resid 63 through 73 Processing helix chain 'H' and resid 77 through 89 Processing helix chain 'H' and resid 107 through 117 removed outlier: 3.569A pdb=" N ASP H 117 " --> pdb=" O ARG H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 135 Processing helix chain 'H' and resid 139 through 146 Processing helix chain 'H' and resid 223 through 230 Processing helix chain 'H' and resid 233 through 251 Processing helix chain 'H' and resid 280 through 285 removed outlier: 3.507A pdb=" N VAL H 285 " --> pdb=" O ASN H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 316 Processing helix chain 'H' and resid 329 through 332 Processing helix chain 'H' and resid 349 through 362 removed outlier: 3.646A pdb=" N GLY H 362 " --> pdb=" O LEU H 358 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 371 Processing helix chain 'I' and resid 38 through 48 Processing helix chain 'I' and resid 52 through 56 Processing helix chain 'I' and resid 63 through 70 removed outlier: 3.670A pdb=" N GLN I 70 " --> pdb=" O ASP I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 89 Processing helix chain 'I' and resid 106 through 117 Processing helix chain 'I' and resid 124 through 136 removed outlier: 3.518A pdb=" N ALA I 136 " --> pdb=" O VAL I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 146 Processing helix chain 'I' and resid 223 through 230 Processing helix chain 'I' and resid 233 through 251 removed outlier: 3.648A pdb=" N ALA I 249 " --> pdb=" O LEU I 245 " (cutoff:3.500A) Processing helix chain 'I' and resid 281 through 285 Processing helix chain 'I' and resid 295 through 316 removed outlier: 3.571A pdb=" N TYR I 316 " --> pdb=" O ARG I 312 " (cutoff:3.500A) Processing helix chain 'I' and resid 329 through 332 Processing helix chain 'I' and resid 349 through 361 Processing helix chain 'I' and resid 365 through 370 removed outlier: 4.051A pdb=" N GLN I 370 " --> pdb=" O TRP I 366 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 48 Processing helix chain 'J' and resid 50 through 54 removed outlier: 3.512A pdb=" N LYS J 53 " --> pdb=" O ASN J 50 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA J 54 " --> pdb=" O ASP J 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 50 through 54' Processing helix chain 'J' and resid 63 through 73 Processing helix chain 'J' and resid 77 through 89 Processing helix chain 'J' and resid 107 through 117 removed outlier: 4.127A pdb=" N LEU J 111 " --> pdb=" O LYS J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 134 removed outlier: 3.783A pdb=" N ALA J 134 " --> pdb=" O ALA J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 137 No H-bonds generated for 'chain 'J' and resid 135 through 137' Processing helix chain 'J' and resid 139 through 145 removed outlier: 3.600A pdb=" N ALA J 143 " --> pdb=" O ALA J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 230 Processing helix chain 'J' and resid 233 through 250 Processing helix chain 'J' and resid 280 through 285 Processing helix chain 'J' and resid 295 through 315 Processing helix chain 'J' and resid 329 through 332 Processing helix chain 'J' and resid 349 through 362 Processing helix chain 'J' and resid 367 through 372 removed outlier: 3.631A pdb=" N GLN J 370 " --> pdb=" O GLU J 367 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 16 removed outlier: 3.622A pdb=" N LEU K 16 " --> pdb=" O PRO K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 48 Processing helix chain 'K' and resid 52 through 56 removed outlier: 3.607A pdb=" N LEU K 56 " --> pdb=" O LYS K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 69 Processing helix chain 'K' and resid 78 through 89 removed outlier: 3.528A pdb=" N GLN K 82 " --> pdb=" O TRP K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 117 Processing helix chain 'K' and resid 121 through 133 Processing helix chain 'K' and resid 139 through 146 Processing helix chain 'K' and resid 223 through 230 Processing helix chain 'K' and resid 234 through 250 Processing helix chain 'K' and resid 280 through 285 Processing helix chain 'K' and resid 296 through 316 Processing helix chain 'K' and resid 328 through 332 Processing helix chain 'K' and resid 349 through 361 removed outlier: 3.557A pdb=" N ASP K 359 " --> pdb=" O GLY K 355 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR K 360 " --> pdb=" O ALA K 356 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE K 361 " --> pdb=" O VAL K 357 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 47 Processing helix chain 'G' and resid 49 through 54 removed outlier: 3.860A pdb=" N LYS G 53 " --> pdb=" O SER G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 229 Processing helix chain 'G' and resid 233 through 251 Processing helix chain 'G' and resid 279 through 285 removed outlier: 4.510A pdb=" N ASN G 282 " --> pdb=" O SER G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 310 Processing helix chain 'G' and resid 329 through 332 Processing helix chain 'G' and resid 349 through 362 Processing helix chain 'B' and resid 36 through 49 Processing helix chain 'B' and resid 60 through 65 removed outlier: 3.861A pdb=" N ASN B 65 " --> pdb=" O PRO B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 157 Processing helix chain 'B' and resid 185 through 193 removed outlier: 3.663A pdb=" N VAL B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 26 through 29 removed outlier: 3.659A pdb=" N VAL F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N SER F 35 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE F 177 " --> pdb=" O TYR F 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 26 through 29 removed outlier: 3.659A pdb=" N VAL F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N SER F 35 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE F 177 " --> pdb=" O TYR F 216 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE F 323 " --> pdb=" O PHE F 273 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ILE F 347 " --> pdb=" O GLY F 324 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N TRP F 326 " --> pdb=" O ILE F 347 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 58 through 61 Processing sheet with id=AA4, first strand: chain 'F' and resid 185 through 191 removed outlier: 3.554A pdb=" N HIS F 204 " --> pdb=" O ALA F 191 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 26 through 29 removed outlier: 5.618A pdb=" N SER H 35 " --> pdb=" O SER H 178 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE H 177 " --> pdb=" O TYR H 216 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 26 through 29 removed outlier: 5.618A pdb=" N SER H 35 " --> pdb=" O SER H 178 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE H 177 " --> pdb=" O TYR H 216 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE H 323 " --> pdb=" O PHE H 273 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG H 345 " --> pdb=" O GLY H 324 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 61 Processing sheet with id=AA8, first strand: chain 'H' and resid 185 through 191 Processing sheet with id=AA9, first strand: chain 'I' and resid 26 through 29 removed outlier: 5.691A pdb=" N SER I 35 " --> pdb=" O SER I 178 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 26 through 29 removed outlier: 5.691A pdb=" N SER I 35 " --> pdb=" O SER I 178 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG I 345 " --> pdb=" O GLY I 324 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 185 through 192 removed outlier: 3.884A pdb=" N PHE I 189 " --> pdb=" O GLY I 206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 26 through 29 removed outlier: 5.481A pdb=" N SER J 35 " --> pdb=" O SER J 178 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE J 177 " --> pdb=" O TYR J 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 26 through 29 removed outlier: 5.481A pdb=" N SER J 35 " --> pdb=" O SER J 178 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE J 177 " --> pdb=" O TYR J 216 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY J 268 " --> pdb=" O ILE J 8 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE J 323 " --> pdb=" O PHE J 273 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLY J 324 " --> pdb=" O ARG J 345 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ILE J 347 " --> pdb=" O GLY J 324 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP J 326 " --> pdb=" O ILE J 347 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 185 through 190 removed outlier: 3.961A pdb=" N PHE J 189 " --> pdb=" O GLY J 206 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY J 206 " --> pdb=" O PHE J 189 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 171 through 173 removed outlier: 3.678A pdb=" N LYS K 274 " --> pdb=" O LEU K 2 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY K 268 " --> pdb=" O ILE K 8 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 26 through 29 removed outlier: 3.550A pdb=" N VAL K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 60 through 61 removed outlier: 3.590A pdb=" N VAL K 101 " --> pdb=" O THR K 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 147 through 148 Processing sheet with id=AC1, first strand: chain 'G' and resid 26 through 29 removed outlier: 5.980A pdb=" N SER G 35 " --> pdb=" O SER G 178 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 26 through 29 removed outlier: 5.980A pdb=" N SER G 35 " --> pdb=" O SER G 178 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY G 268 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N GLY G 324 " --> pdb=" O ARG G 345 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ILE G 347 " --> pdb=" O GLY G 324 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP G 326 " --> pdb=" O ILE G 347 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 185 through 188 Processing sheet with id=AC4, first strand: chain 'B' and resid 7 through 17 removed outlier: 6.945A pdb=" N THR B 7 " --> pdb=" O GLN B 142 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLN B 142 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE B 9 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA B 140 " --> pdb=" O PHE B 9 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ARG B 11 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU B 138 " --> pdb=" O ARG B 11 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLU B 13 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N SER B 136 " --> pdb=" O GLU B 13 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ALA B 15 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 77 " --> pdb=" O ALA B 133 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 28 through 29 removed outlier: 6.866A pdb=" N SER B 136 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N MET B 68 " --> pdb=" O ASP B 213 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N ARG B 241 " --> pdb=" O PRO B 234 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU B 243 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP B 232 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B 228 " --> pdb=" O VAL B 247 " (cutoff:3.500A) 818 hydrogen bonds defined for protein. 2241 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 3.68 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5997 1.34 - 1.45: 3372 1.45 - 1.57: 10218 1.57 - 1.69: 147 1.69 - 1.81: 110 Bond restraints: 19844 Sorted by residual: bond pdb=" C3' DT M 49 " pdb=" C2' DT M 49 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C1' DC M 38 " pdb=" N1 DC M 38 " ideal model delta sigma weight residual 1.468 1.505 -0.037 1.40e-02 5.10e+03 7.08e+00 bond pdb=" C1' DT M 32 " pdb=" N1 DT M 32 " ideal model delta sigma weight residual 1.468 1.504 -0.036 1.40e-02 5.10e+03 6.44e+00 bond pdb=" C1' DT M 35 " pdb=" N1 DT M 35 " ideal model delta sigma weight residual 1.468 1.503 -0.035 1.40e-02 5.10e+03 6.27e+00 bond pdb=" C3' DC M 26 " pdb=" C2' DC M 26 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.00e+00 ... (remaining 19839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 26907 2.39 - 4.79: 301 4.79 - 7.18: 37 7.18 - 9.58: 9 9.58 - 11.97: 2 Bond angle restraints: 27256 Sorted by residual: angle pdb=" C1' C A 24 " pdb=" N1 C A 24 " pdb=" C2 C A 24 " ideal model delta sigma weight residual 118.80 127.78 -8.98 1.10e+00 8.26e-01 6.67e+01 angle pdb=" N1 C A 24 " pdb=" C2 C A 24 " pdb=" O2 C A 24 " ideal model delta sigma weight residual 118.90 123.62 -4.72 6.00e-01 2.78e+00 6.20e+01 angle pdb=" O2 C A 24 " pdb=" C2 C A 24 " pdb=" N3 C A 24 " ideal model delta sigma weight residual 121.90 117.45 4.45 7.00e-01 2.04e+00 4.04e+01 angle pdb=" C1' C A 24 " pdb=" N1 C A 24 " pdb=" C6 C A 24 " ideal model delta sigma weight residual 120.80 114.04 6.76 1.20e+00 6.94e-01 3.18e+01 angle pdb=" C2 C A 24 " pdb=" N1 C A 24 " pdb=" C6 C A 24 " ideal model delta sigma weight residual 120.30 118.14 2.16 4.00e-01 6.25e+00 2.90e+01 ... (remaining 27251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.10: 10585 27.10 - 54.19: 1059 54.19 - 81.29: 174 81.29 - 108.38: 20 108.38 - 135.48: 1 Dihedral angle restraints: 11839 sinusoidal: 5145 harmonic: 6694 Sorted by residual: dihedral pdb=" O4' C A 6 " pdb=" C1' C A 6 " pdb=" N1 C A 6 " pdb=" C2 C A 6 " ideal model delta sinusoidal sigma weight residual 200.00 64.52 135.48 1 1.50e+01 4.44e-03 7.31e+01 dihedral pdb=" O4' C A 24 " pdb=" C1' C A 24 " pdb=" N1 C A 24 " pdb=" C2 C A 24 " ideal model delta sinusoidal sigma weight residual 200.00 101.13 98.87 1 1.50e+01 4.44e-03 4.92e+01 dihedral pdb=" O4' C A 7 " pdb=" C1' C A 7 " pdb=" N1 C A 7 " pdb=" C2 C A 7 " ideal model delta sinusoidal sigma weight residual -128.00 -22.75 -105.25 1 1.70e+01 3.46e-03 4.20e+01 ... (remaining 11836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2501 0.051 - 0.103: 470 0.103 - 0.154: 91 0.154 - 0.205: 3 0.205 - 0.257: 2 Chirality restraints: 3067 Sorted by residual: chirality pdb=" CG LEU B 44 " pdb=" CB LEU B 44 " pdb=" CD1 LEU B 44 " pdb=" CD2 LEU B 44 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA PRO J 151 " pdb=" N PRO J 151 " pdb=" C PRO J 151 " pdb=" CB PRO J 151 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB THR K 165 " pdb=" CA THR K 165 " pdb=" OG1 THR K 165 " pdb=" CG2 THR K 165 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.38e-01 ... (remaining 3064 not shown) Planarity restraints: 3299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU J 150 " -0.075 5.00e-02 4.00e+02 1.14e-01 2.07e+01 pdb=" N PRO J 151 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO J 151 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO J 151 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 238 " 0.045 5.00e-02 4.00e+02 6.87e-02 7.55e+00 pdb=" N PRO B 239 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 239 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 239 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 150 " 0.042 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO F 151 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO F 151 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 151 " 0.035 5.00e-02 4.00e+02 ... (remaining 3296 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 388 2.66 - 3.22: 17283 3.22 - 3.78: 30643 3.78 - 4.34: 41067 4.34 - 4.90: 67730 Nonbonded interactions: 157111 Sorted by model distance: nonbonded pdb=" OE2 GLU J 272 " pdb=" NZ LYS J 274 " model vdw 2.098 3.120 nonbonded pdb=" OE2 GLU I 4 " pdb=" OH TYR I 218 " model vdw 2.159 3.040 nonbonded pdb=" O2' C A 7 " pdb=" NH1 ARG F 18 " model vdw 2.161 3.120 nonbonded pdb=" OD1 ASP J 187 " pdb=" NH1 ARG K 36 " model vdw 2.165 3.120 nonbonded pdb=" O2' U A -6 " pdb=" OG SER B 38 " model vdw 2.173 3.040 ... (remaining 157106 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'F' and (resid 1 through 52 or (resid 53 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 69 or (resid 70 and (nam \ e N or name CA or name C or name O or name CB )) or resid 71 through 74 or (resi \ d 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throug \ h 78 or (resid 79 through 81 and (name N or name CA or name C or name O or name \ CB )) or resid 82 or (resid 83 and (name N or name CA or name C or name O or nam \ e CB )) or resid 84 through 86 or (resid 87 and (name N or name CA or name C or \ name O or name CB )) or resid 88 through 98 or (resid 99 and (name N or name CA \ or name C or name O or name CB )) or resid 100 through 104 or (resid 105 and (na \ me N or name CA or name C or name O or name CB )) or resid 106 through 117 or (r \ esid 118 and (name N or name CA or name C or name O or name CB )) or resid 119 o \ r (resid 120 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 21 or (resid 122 through 126 and (name N or name CA or name C or name O or name \ CB )) or resid 127 through 155 or (resid 156 and (name N or name CA or name C or \ name O or name CB )) or resid 157 through 159 or (resid 160 through 161 and (na \ me N or name CA or name C or name O or name CB )) or resid 162 through 184 or re \ sid 208 through 225 or (resid 226 and (name N or name CA or name C or name O or \ name CB )) or resid 227 or (resid 228 and (name N or name CA or name C or name O \ or name CB )) or resid 229 through 230 or (resid 231 and (name N or name CA or \ name C or name O or name CB )) or resid 232 through 256 or resid 263 through 291 \ or (resid 292 and (name N or name CA or name C or name O or name CB )) or resid \ 293 through 315 or (resid 316 through 319 and (name N or name CA or name C or n \ ame O or name CB )) or resid 320 through 338 or (resid 339 and (name N or name C \ A or name C or name O or name CB )) or resid 340 or (resid 341 and (name N or na \ me CA or name C or name O or name CB )) or resid 342 through 351 or (resid 352 a \ nd (name N or name CA or name C or name O or name CB )) or resid 353 through 368 \ or (resid 369 and (name N or name CA or name C or name O or name CB )) or resid \ 370 through 372)) selection = (chain 'H' and (resid 1 through 52 or (resid 53 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 69 or (resid 70 and (nam \ e N or name CA or name C or name O or name CB )) or resid 71 through 74 or (resi \ d 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throug \ h 79 or (resid 80 through 81 and (name N or name CA or name C or name O or name \ CB )) or resid 82 or (resid 83 and (name N or name CA or name C or name O or nam \ e CB )) or resid 84 through 90 or (resid 91 and (name N or name CA or name C or \ name O or name CB )) or resid 92 or resid 97 or (resid 98 through 99 and (name N \ or name CA or name C or name O or name CB )) or resid 100 through 104 or (resid \ 105 and (name N or name CA or name C or name O or name CB )) or resid 106 throu \ gh 117 or (resid 118 and (name N or name CA or name C or name O or name CB )) or \ resid 119 through 121 or (resid 122 through 126 and (name N or name CA or name \ C or name O or name CB )) or resid 127 through 152 or (resid 153 through 154 and \ (name N or name CA or name C or name O or name CB )) or resid 155 or (resid 156 \ and (name N or name CA or name C or name O or name CB )) or resid 157 through 1 \ 59 or (resid 160 through 161 and (name N or name CA or name C or name O or name \ CB )) or resid 162 through 184 or resid 208 through 225 or (resid 226 and (name \ N or name CA or name C or name O or name CB )) or resid 227 or (resid 228 and (n \ ame N or name CA or name C or name O or name CB )) or resid 229 through 230 or ( \ resid 231 and (name N or name CA or name C or name O or name CB )) or resid 232 \ through 256 or resid 263 through 291 or (resid 292 and (name N or name CA or nam \ e C or name O or name CB )) or resid 293 through 311 or (resid 312 and (name N o \ r name CA or name C or name O or name CB )) or resid 313 through 316 or (resid 3 \ 17 through 319 and (name N or name CA or name C or name O or name CB )) or resid \ 320 through 338 or (resid 339 and (name N or name CA or name C or name O or nam \ e CB )) or resid 340 or (resid 341 and (name N or name CA or name C or name O or \ name CB )) or resid 342 through 351 or (resid 352 and (name N or name CA or nam \ e C or name O or name CB )) or resid 353 through 364 or (resid 365 and (name N o \ r name CA or name C or name O or name CB )) or resid 366 through 367 or (resid 3 \ 68 through 369 and (name N or name CA or name C or name O or name CB )) or resid \ 370 through 372)) selection = (chain 'I' and (resid 1 through 52 or (resid 53 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 74 or (resid 75 and (nam \ e N or name CA or name C or name O or name CB )) or resid 76 through 78 or (resi \ d 79 through 81 and (name N or name CA or name C or name O or name CB )) or resi \ d 82 or (resid 83 and (name N or name CA or name C or name O or name CB )) or re \ sid 84 through 86 or (resid 87 and (name N or name CA or name C or name O or nam \ e CB )) or resid 88 through 90 or (resid 91 and (name N or name CA or name C or \ name O or name CB )) or resid 92 or resid 97 or (resid 98 through 99 and (name N \ or name CA or name C or name O or name CB )) or resid 100 through 104 or (resid \ 105 and (name N or name CA or name C or name O or name CB )) or resid 106 throu \ gh 108 or (resid 109 and (name N or name CA or name C or name O or name CB )) or \ resid 110 through 117 or (resid 118 and (name N or name CA or name C or name O \ or name CB )) or resid 119 or (resid 120 and (name N or name CA or name C or nam \ e O or name CB )) or resid 121 through 159 or (resid 160 through 161 and (name N \ or name CA or name C or name O or name CB )) or resid 162 through 184 or resid \ 208 through 225 or (resid 226 and (name N or name CA or name C or name O or name \ CB )) or resid 227 or (resid 228 and (name N or name CA or name C or name O or \ name CB )) or resid 229 through 256 or resid 263 through 311 or (resid 312 and ( \ name N or name CA or name C or name O or name CB )) or resid 313 through 315 or \ (resid 316 through 319 and (name N or name CA or name C or name O or name CB )) \ or resid 320 through 338 or (resid 339 and (name N or name CA or name C or name \ O or name CB )) or resid 340 through 351 or (resid 352 and (name N or name CA or \ name C or name O or name CB )) or resid 353 through 364 or (resid 365 and (name \ N or name CA or name C or name O or name CB )) or resid 366 through 367 or (res \ id 368 through 369 and (name N or name CA or name C or name O or name CB )) or r \ esid 370 or (resid 371 and (name N or name CA or name C or name O or name CB )) \ or resid 372)) selection = (chain 'J' and (resid 1 through 52 or (resid 53 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 69 or (resid 70 and (nam \ e N or name CA or name C or name O or name CB )) or resid 71 through 79 or (resi \ d 80 through 81 and (name N or name CA or name C or name O or name CB )) or resi \ d 82 through 86 or (resid 87 and (name N or name CA or name C or name O or name \ CB )) or resid 88 through 90 or (resid 91 and (name N or name CA or name C or na \ me O or name CB )) or resid 92 or resid 97 through 98 or (resid 99 and (name N o \ r name CA or name C or name O or name CB )) or resid 100 through 108 or (resid 1 \ 09 and (name N or name CA or name C or name O or name CB )) or resid 110 through \ 121 or (resid 122 through 126 and (name N or name CA or name C or name O or nam \ e CB )) or resid 127 through 152 or (resid 153 through 154 and (name N or name C \ A or name C or name O or name CB )) or resid 155 or (resid 156 and (name N or na \ me CA or name C or name O or name CB )) or resid 157 or (resid 158 through 161 a \ nd (name N or name CA or name C or name O or name CB )) or resid 162 through 184 \ or resid 208 through 225 or (resid 226 and (name N or name CA or name C or name \ O or name CB )) or resid 227 through 230 or (resid 231 and (name N or name CA o \ r name C or name O or name CB )) or resid 232 through 256 or resid 263 through 3 \ 11 or (resid 312 and (name N or name CA or name C or name O or name CB )) or res \ id 313 through 315 or (resid 316 through 319 and (name N or name CA or name C or \ name O or name CB )) or resid 320 through 351 or (resid 352 and (name N or name \ CA or name C or name O or name CB )) or resid 353 through 367 or (resid 368 thr \ ough 369 and (name N or name CA or name C or name O or name CB )) or resid 370 o \ r (resid 371 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 72)) selection = (chain 'K' and (resid 1 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 74 or (resid 75 and (name N or name \ CA or name C or name O or name CB )) or resid 76 through 78 or (resid 79 throug \ h 81 and (name N or name CA or name C or name O or name CB )) or resid 82 or (re \ sid 83 and (name N or name CA or name C or name O or name CB )) or resid 84 thro \ ugh 86 or (resid 87 and (name N or name CA or name C or name O or name CB )) or \ resid 88 through 90 or (resid 91 and (name N or name CA or name C or name O or n \ ame CB )) or resid 92 or resid 97 or (resid 98 through 99 and (name N or name CA \ or name C or name O or name CB )) or resid 100 through 104 or (resid 105 and (n \ ame N or name CA or name C or name O or name CB )) or resid 106 through 108 or ( \ resid 109 and (name N or name CA or name C or name O or name CB )) or resid 110 \ through 117 or (resid 118 and (name N or name CA or name C or name O or name CB \ )) or resid 119 or (resid 120 and (name N or name CA or name C or name O or name \ CB )) or resid 121 or (resid 122 through 126 and (name N or name CA or name C o \ r name O or name CB )) or resid 127 through 152 or (resid 153 through 154 and (n \ ame N or name CA or name C or name O or name CB )) or resid 155 or (resid 156 an \ d (name N or name CA or name C or name O or name CB )) or resid 157 through 159 \ or (resid 160 through 161 and (name N or name CA or name C or name O or name CB \ )) or resid 162 through 227 or (resid 228 and (name N or name CA or name C or na \ me O or name CB )) or resid 229 through 291 or (resid 292 and (name N or name CA \ or name C or name O or name CB )) or resid 293 through 311 or (resid 312 and (n \ ame N or name CA or name C or name O or name CB )) or resid 313 through 316 or ( \ resid 317 through 319 and (name N or name CA or name C or name O or name CB )) o \ r resid 320 through 338 or (resid 339 and (name N or name CA or name C or name O \ or name CB )) or resid 340 or (resid 341 and (name N or name CA or name C or na \ me O or name CB )) or resid 342 through 367 or (resid 368 through 369 and (name \ N or name CA or name C or name O or name CB )) or resid 370 through 372)) } 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 individual isotropic 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: 4.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 20.780 Find NCS groups from input model: 0.380 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: 0.000 Load rotamer database and sin/cos tables:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 : 0.004 0.114 19844 Z= 0.209 Angle : 0.643 11.975 27256 Z= 0.404 Chirality : 0.042 0.257 3067 Planarity : 0.005 0.114 3299 Dihedral : 20.457 135.476 7519 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.03 % Favored : 93.84 % Rotamer: Outliers : 2.60 % Allowed : 35.77 % Favored : 61.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.18), residues: 2288 helix: 1.34 (0.20), residues: 769 sheet: 1.10 (0.24), residues: 434 loop : -1.12 (0.20), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 286 TYR 0.025 0.001 TYR J 360 PHE 0.021 0.001 PHE B 82 TRP 0.037 0.001 TRP B 59 HIS 0.003 0.001 HIS J 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.21 (19844) covalent geometry : angle 0.64312 / 0.40 (27256) hydrogen bonds : bond 0.18395 / 18.74 ( 806) hydrogen bonds : angle 6.50419 / 6.43 ( 2299) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 436 time to evaluate : 0.693 Fit side-chains REVERT: F 18 ARG cc_start: 0.8190 (ptt90) cc_final: 0.7943 (ptt90) REVERT: J 168 GLU cc_start: 0.6893 (tp30) cc_final: 0.6559 (mp0) REVERT: J 251 THR cc_start: 0.8099 (t) cc_final: 0.7889 (m) REVERT: J 274 LYS cc_start: 0.7296 (ptpt) cc_final: 0.7019 (pttt) REVERT: K 18 ARG cc_start: 0.7361 (mpt180) cc_final: 0.7060 (mmt180) REVERT: K 160 VAL cc_start: 0.8457 (m) cc_final: 0.8237 (p) REVERT: K 209 MET cc_start: 0.2307 (mmm) cc_final: 0.0744 (tmt) outliers start: 48 outliers final: 36 residues processed: 474 average time/residue: 0.5747 time to fit residues: 309.1282 Evaluate side-chains 463 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 427 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 124 GLU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 150 GLU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain J residue 74 GLU Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 276 SER Chi-restraints excluded: chain K residue 309 ASN Chi-restraints excluded: chain K residue 338 LYS Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 361 ILE Chi-restraints excluded: chain G residue 172 GLN Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 286 ARG Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 168 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0470 chunk 200 optimal weight: 0.3980 overall best weight: 0.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 17 ASN ** F 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN H 164 ASN H 252 ASN H 370 GLN I 17 ASN I 82 GLN I 127 GLN I 204 HIS I 306 ASN J 17 ASN J 303 GLN J 349 ASN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.154700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.130030 restraints weight = 28029.674| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.21 r_work: 0.3611 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.0746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 19844 Z= 0.148 Angle : 0.599 11.037 27256 Z= 0.322 Chirality : 0.043 0.339 3067 Planarity : 0.005 0.115 3299 Dihedral : 16.876 137.608 3539 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.81 % Favored : 94.10 % Rotamer: Outliers : 4.71 % Allowed : 30.36 % Favored : 64.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.18), residues: 2288 helix: 1.33 (0.20), residues: 782 sheet: 1.32 (0.24), residues: 396 loop : -1.11 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 113 TYR 0.019 0.001 TYR I 265 PHE 0.013 0.001 PHE J 189 TRP 0.021 0.001 TRP B 59 HIS 0.003 0.001 HIS I 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (19844) covalent geometry : angle 0.59886 / 0.32 (27256) hydrogen bonds : bond 0.04459 / 4.42 ( 806) hydrogen bonds : angle 4.83724 / 4.95 ( 2299) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 441 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: F 103 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.6425 (pp-130) REVERT: F 127 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7466 (tm-30) REVERT: F 209 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7859 (mtm) REVERT: F 250 LYS cc_start: 0.8510 (mtmm) cc_final: 0.8305 (mtmm) REVERT: H 209 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7661 (mtm) REVERT: H 218 TYR cc_start: 0.8647 (t80) cc_final: 0.8205 (t80) REVERT: H 256 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8083 (mttt) REVERT: I 111 LEU cc_start: 0.7697 (mm) cc_final: 0.7437 (mm) REVERT: I 209 MET cc_start: 0.8112 (mtm) cc_final: 0.7871 (mpp) REVERT: J 86 ASN cc_start: 0.8098 (m-40) cc_final: 0.7876 (m110) REVERT: J 168 GLU cc_start: 0.7515 (tp30) cc_final: 0.7215 (mp0) REVERT: J 330 ASN cc_start: 0.7923 (t0) cc_final: 0.7588 (t0) REVERT: K 18 ARG cc_start: 0.7241 (mpt180) cc_final: 0.6858 (mpt180) REVERT: K 209 MET cc_start: 0.2472 (mmm) cc_final: 0.1025 (tmt) REVERT: K 338 LYS cc_start: -0.0734 (OUTLIER) cc_final: -0.1240 (mttp) REVERT: B 68 MET cc_start: 0.7441 (ttt) cc_final: 0.7192 (ttt) outliers start: 87 outliers final: 42 residues processed: 488 average time/residue: 0.5579 time to fit residues: 309.1199 Evaluate side-chains 478 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 431 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 148 MET Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 209 MET Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 256 LYS Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 361 ILE Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 103 MET Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 145 CYS Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain K residue 338 LYS Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 353 LEU Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 286 ARG Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 191 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 98 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 201 optimal weight: 0.0670 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 212 optimal weight: 0.0770 chunk 90 optimal weight: 2.9990 overall best weight: 1.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 180 HIS ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN H 131 ASN H 164 ASN I 17 ASN I 127 GLN I 306 ASN J 17 ASN J 69 GLN J 204 HIS ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 ASN ** K 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 235 ASN K 349 ASN G 172 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.149708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.125219 restraints weight = 27950.532| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.20 r_work: 0.3534 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 19844 Z= 0.225 Angle : 0.642 10.201 27256 Z= 0.346 Chirality : 0.046 0.297 3067 Planarity : 0.005 0.116 3299 Dihedral : 16.912 136.567 3500 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.12 % Favored : 93.79 % Rotamer: Outliers : 7.58 % Allowed : 27.38 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.18), residues: 2288 helix: 1.12 (0.19), residues: 779 sheet: 0.93 (0.24), residues: 408 loop : -1.21 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 18 TYR 0.018 0.002 TYR I 265 PHE 0.023 0.002 PHE J 189 TRP 0.040 0.002 TRP B 59 HIS 0.006 0.001 HIS K 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.22 (19844) covalent geometry : angle 0.64169 / 0.35 (27256) hydrogen bonds : bond 0.04427 / 4.36 ( 806) hydrogen bonds : angle 4.59464 / 4.87 ( 2299) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 453 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 52 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.7327 (m-80) REVERT: F 63 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.8121 (mtt-85) REVERT: F 103 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.6375 (pp-130) REVERT: F 127 GLN cc_start: 0.7964 (mm-40) cc_final: 0.7680 (tm-30) REVERT: F 209 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7911 (mtm) REVERT: H 122 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7625 (tm) REVERT: I 111 LEU cc_start: 0.7848 (mm) cc_final: 0.7604 (mm) REVERT: I 150 GLU cc_start: 0.7306 (mp0) cc_final: 0.6949 (tt0) REVERT: J 135 GLN cc_start: 0.7868 (mt0) cc_final: 0.7625 (mt0) REVERT: J 168 GLU cc_start: 0.7609 (tp30) cc_final: 0.7348 (mp0) REVERT: J 251 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7890 (m) REVERT: J 272 GLU cc_start: 0.7452 (pt0) cc_final: 0.7193 (pt0) REVERT: J 278 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7643 (mt) REVERT: K 18 ARG cc_start: 0.7431 (mpt180) cc_final: 0.7117 (mpt180) REVERT: K 103 MET cc_start: 0.6881 (mmt) cc_final: 0.5821 (mmt) REVERT: K 131 ASN cc_start: 0.8150 (t0) cc_final: 0.7758 (t0) REVERT: K 246 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8034 (mp) REVERT: G 342 LEU cc_start: 0.1525 (OUTLIER) cc_final: 0.1180 (mp) REVERT: B 68 MET cc_start: 0.7545 (ttt) cc_final: 0.7274 (ttt) outliers start: 140 outliers final: 61 residues processed: 522 average time/residue: 0.5215 time to fit residues: 309.7967 Evaluate side-chains 494 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 424 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 275 ASN Chi-restraints excluded: chain F residue 292 LYS Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 148 MET Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 256 LYS Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 91 LYS Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 103 MET Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 145 CYS Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 246 LEU Chi-restraints excluded: chain K residue 296 LEU Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 353 LEU Chi-restraints excluded: chain K residue 361 ILE Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 172 GLN Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 212 SER Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 243 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 101 optimal weight: 0.5980 chunk 114 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 202 optimal weight: 0.0980 chunk 156 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN H 131 ASN H 164 ASN I 17 ASN I 127 GLN I 306 ASN J 17 ASN J 69 GLN J 86 ASN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 ASN K 131 ASN ** K 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 235 ASN K 303 GLN K 349 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.150456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.126154 restraints weight = 27936.626| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.18 r_work: 0.3547 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 19844 Z= 0.160 Angle : 0.593 10.222 27256 Z= 0.318 Chirality : 0.043 0.281 3067 Planarity : 0.004 0.115 3299 Dihedral : 16.795 137.957 3487 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.86 % Favored : 94.06 % Rotamer: Outliers : 5.63 % Allowed : 29.60 % Favored : 64.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.18), residues: 2288 helix: 1.17 (0.19), residues: 787 sheet: 0.85 (0.24), residues: 404 loop : -1.19 (0.19), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 286 TYR 0.019 0.001 TYR I 265 PHE 0.020 0.001 PHE J 189 TRP 0.031 0.001 TRP B 59 HIS 0.004 0.001 HIS K 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (19844) covalent geometry : angle 0.59320 / 0.32 (27256) hydrogen bonds : bond 0.03769 / 3.73 ( 806) hydrogen bonds : angle 4.43165 / 4.68 ( 2299) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 439 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 52 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7166 (m-80) REVERT: F 63 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7977 (mtt-85) REVERT: F 103 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.6538 (pp-130) REVERT: F 127 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7650 (tm-30) REVERT: H 122 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7573 (tm) REVERT: H 218 TYR cc_start: 0.8561 (t80) cc_final: 0.8240 (t80) REVERT: H 256 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8022 (mttt) REVERT: I 111 LEU cc_start: 0.7764 (mm) cc_final: 0.7514 (mm) REVERT: I 150 GLU cc_start: 0.7220 (mp0) cc_final: 0.6924 (tt0) REVERT: I 365 LYS cc_start: 0.8096 (mmtm) cc_final: 0.7851 (mtpp) REVERT: J 135 GLN cc_start: 0.7981 (mt0) cc_final: 0.7683 (mt0) REVERT: J 168 GLU cc_start: 0.7627 (tp30) cc_final: 0.7359 (mp0) REVERT: J 251 THR cc_start: 0.8114 (OUTLIER) cc_final: 0.7863 (m) REVERT: J 272 GLU cc_start: 0.7393 (pt0) cc_final: 0.7189 (pt0) REVERT: J 278 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7598 (mt) REVERT: K 4 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: K 18 ARG cc_start: 0.7343 (mpt180) cc_final: 0.6742 (mpt180) REVERT: K 103 MET cc_start: 0.6827 (mmt) cc_final: 0.5552 (mmt) REVERT: K 131 ASN cc_start: 0.8124 (OUTLIER) cc_final: 0.7696 (t0) REVERT: K 209 MET cc_start: 0.2375 (mmm) cc_final: 0.0597 (tmt) REVERT: K 246 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8047 (mp) REVERT: G 1 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7287 (ppp) REVERT: G 342 LEU cc_start: 0.1634 (OUTLIER) cc_final: 0.1228 (mp) REVERT: B 68 MET cc_start: 0.7515 (ttt) cc_final: 0.7242 (ttt) outliers start: 104 outliers final: 56 residues processed: 492 average time/residue: 0.5639 time to fit residues: 315.6562 Evaluate side-chains 500 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 432 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 275 ASN Chi-restraints excluded: chain F residue 292 LYS Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 148 MET Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 256 LYS Chi-restraints excluded: chain I residue 91 LYS Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 103 MET Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain K residue 4 GLU Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain K residue 246 LEU Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 296 LEU Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 353 LEU Chi-restraints excluded: chain K residue 361 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 212 SER Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 247 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 125 optimal weight: 0.9990 chunk 232 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 204 HIS H 17 ASN H 86 ASN H 164 ASN I 17 ASN I 127 GLN I 152 ASN I 306 ASN J 17 ASN J 69 GLN J 225 GLN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 ASN K 131 ASN ** K 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 349 ASN G 172 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.148317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.124037 restraints weight = 27816.681| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.18 r_work: 0.3517 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 19844 Z= 0.220 Angle : 0.615 11.257 27256 Z= 0.330 Chirality : 0.045 0.266 3067 Planarity : 0.004 0.115 3299 Dihedral : 16.847 139.033 3487 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.12 % Favored : 93.79 % Rotamer: Outliers : 6.01 % Allowed : 28.90 % Favored : 65.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.18), residues: 2288 helix: 1.13 (0.19), residues: 781 sheet: 0.70 (0.24), residues: 409 loop : -1.24 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 286 TYR 0.019 0.001 TYR I 265 PHE 0.023 0.002 PHE J 189 TRP 0.027 0.002 TRP B 59 HIS 0.005 0.001 HIS K 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.22 (19844) covalent geometry : angle 0.61505 / 0.33 (27256) hydrogen bonds : bond 0.03998 / 3.96 ( 806) hydrogen bonds : angle 4.44438 / 4.72 ( 2299) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 422 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 52 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7126 (m-80) REVERT: F 62 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7919 (ptp-170) REVERT: F 63 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8023 (mtt-85) REVERT: F 103 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.6507 (pp-130) REVERT: F 147 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7758 (ptt90) REVERT: F 209 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7907 (mtm) REVERT: H 122 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7540 (tm) REVERT: I 1 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8214 (ptm) REVERT: I 111 LEU cc_start: 0.7822 (mm) cc_final: 0.7596 (mm) REVERT: I 365 LYS cc_start: 0.8140 (mmtm) cc_final: 0.7877 (mtpp) REVERT: J 135 GLN cc_start: 0.7965 (mt0) cc_final: 0.7689 (mt0) REVERT: J 168 GLU cc_start: 0.7622 (tp30) cc_final: 0.7358 (mp0) REVERT: J 251 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7890 (m) REVERT: J 278 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7600 (mt) REVERT: K 4 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7934 (mt-10) REVERT: K 18 ARG cc_start: 0.7413 (mpt180) cc_final: 0.6937 (mpt180) REVERT: K 35 SER cc_start: 0.8387 (OUTLIER) cc_final: 0.8151 (m) REVERT: K 103 MET cc_start: 0.6957 (mmt) cc_final: 0.5620 (mmt) REVERT: K 131 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7909 (t0) REVERT: K 246 LEU cc_start: 0.8365 (mm) cc_final: 0.8057 (mp) REVERT: K 368 GLU cc_start: 0.7467 (pp20) cc_final: 0.6984 (pp20) REVERT: G 1 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7263 (ppp) REVERT: B 54 GLU cc_start: 0.6356 (OUTLIER) cc_final: 0.6099 (mp0) REVERT: B 63 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7315 (mp) REVERT: B 68 MET cc_start: 0.7542 (ttt) cc_final: 0.7281 (ttt) outliers start: 111 outliers final: 65 residues processed: 474 average time/residue: 0.5884 time to fit residues: 316.9593 Evaluate side-chains 501 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 420 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 275 ASN Chi-restraints excluded: chain F residue 292 LYS Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 148 MET Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 256 LYS Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 91 LYS Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 103 MET Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 145 CYS Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain K residue 4 GLU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 296 LEU Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 353 LEU Chi-restraints excluded: chain K residue 361 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 172 GLN Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 212 SER Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 247 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 82 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 208 optimal weight: 0.0770 chunk 89 optimal weight: 0.9990 chunk 193 optimal weight: 0.5980 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 17 ASN H 86 ASN H 164 ASN I 17 ASN I 127 GLN I 152 ASN I 306 ASN J 17 ASN J 69 GLN J 86 ASN J 127 GLN J 349 ASN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 ASN K 131 ASN ** K 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 349 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.148918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.124754 restraints weight = 27680.067| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.16 r_work: 0.3527 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 19844 Z= 0.163 Angle : 0.587 9.780 27256 Z= 0.315 Chirality : 0.043 0.245 3067 Planarity : 0.004 0.114 3299 Dihedral : 16.774 139.833 3487 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.99 % Favored : 93.92 % Rotamer: Outliers : 6.06 % Allowed : 28.79 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.18), residues: 2288 helix: 1.20 (0.19), residues: 787 sheet: 0.70 (0.24), residues: 409 loop : -1.18 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 286 TYR 0.018 0.001 TYR I 265 PHE 0.022 0.001 PHE J 189 TRP 0.029 0.001 TRP B 59 HIS 0.004 0.001 HIS K 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (19844) covalent geometry : angle 0.58713 / 0.31 (27256) hydrogen bonds : bond 0.03703 / 3.73 ( 806) hydrogen bonds : angle 4.37094 / 4.62 ( 2299) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 430 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 52 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7120 (m-80) REVERT: F 62 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7929 (ptp-170) REVERT: F 63 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7939 (mtt-85) REVERT: F 107 LYS cc_start: 0.7592 (tppp) cc_final: 0.7123 (tppp) REVERT: F 127 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7726 (tm-30) REVERT: F 147 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7721 (ptt90) REVERT: F 209 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.7905 (mtm) REVERT: H 122 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7498 (tm) REVERT: H 218 TYR cc_start: 0.8539 (t80) cc_final: 0.8278 (t80) REVERT: H 256 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7990 (mttt) REVERT: I 111 LEU cc_start: 0.7783 (mm) cc_final: 0.7561 (mm) REVERT: I 148 MET cc_start: 0.8416 (tmt) cc_final: 0.8153 (tmt) REVERT: I 365 LYS cc_start: 0.8154 (mmtm) cc_final: 0.7751 (mtpp) REVERT: I 368 GLU cc_start: 0.7724 (pm20) cc_final: 0.7466 (pm20) REVERT: J 135 GLN cc_start: 0.7952 (mt0) cc_final: 0.7666 (mt0) REVERT: J 168 GLU cc_start: 0.7628 (tp30) cc_final: 0.7369 (mp0) REVERT: J 251 THR cc_start: 0.8132 (OUTLIER) cc_final: 0.7877 (m) REVERT: J 278 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7650 (mt) REVERT: K 4 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7955 (mt-10) REVERT: K 18 ARG cc_start: 0.7449 (mpt180) cc_final: 0.6839 (mpt180) REVERT: K 103 MET cc_start: 0.6839 (mmt) cc_final: 0.5530 (mmt) REVERT: K 131 ASN cc_start: 0.8245 (OUTLIER) cc_final: 0.7930 (t0) REVERT: K 209 MET cc_start: 0.2050 (mmm) cc_final: 0.0303 (tmt) REVERT: K 368 GLU cc_start: 0.7505 (pp20) cc_final: 0.7025 (pp20) REVERT: G 1 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7240 (ppp) REVERT: G 342 LEU cc_start: 0.1779 (OUTLIER) cc_final: 0.1396 (mp) REVERT: G 345 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7743 (mtm110) REVERT: B 54 GLU cc_start: 0.6346 (OUTLIER) cc_final: 0.6094 (mp0) REVERT: B 63 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7285 (mp) REVERT: B 68 MET cc_start: 0.7502 (ttt) cc_final: 0.7247 (ttt) REVERT: B 78 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6881 (mtt180) outliers start: 112 outliers final: 59 residues processed: 488 average time/residue: 0.5912 time to fit residues: 327.2725 Evaluate side-chains 491 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 415 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 275 ASN Chi-restraints excluded: chain F residue 292 LYS Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 256 LYS Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 91 LYS Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 208 SER Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 103 MET Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 145 CYS Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain K residue 4 GLU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 299 GLN Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 353 LEU Chi-restraints excluded: chain K residue 361 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 212 SER Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 243 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 82 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 163 optimal weight: 6.9990 chunk 202 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 174 optimal weight: 0.0020 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 17 ASN H 86 ASN H 164 ASN I 17 ASN I 127 GLN I 152 ASN I 349 ASN J 17 ASN J 69 GLN J 127 GLN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 131 ASN ** K 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 349 ASN G 172 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.149228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.124907 restraints weight = 27769.846| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.18 r_work: 0.3532 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 19844 Z= 0.145 Angle : 0.580 10.295 27256 Z= 0.309 Chirality : 0.043 0.234 3067 Planarity : 0.004 0.113 3299 Dihedral : 16.744 140.699 3487 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.94 % Favored : 93.97 % Rotamer: Outliers : 6.06 % Allowed : 29.17 % Favored : 64.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.18), residues: 2288 helix: 1.26 (0.19), residues: 787 sheet: 0.71 (0.24), residues: 409 loop : -1.16 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 18 TYR 0.018 0.001 TYR I 265 PHE 0.021 0.001 PHE J 189 TRP 0.032 0.001 TRP B 59 HIS 0.004 0.001 HIS K 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (19844) covalent geometry : angle 0.58039 / 0.31 (27256) hydrogen bonds : bond 0.03546 / 3.56 ( 806) hydrogen bonds : angle 4.31095 / 4.55 ( 2299) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 423 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 52 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7121 (m-80) REVERT: F 62 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7906 (ptp-170) REVERT: F 63 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7902 (mtt-85) REVERT: F 127 GLN cc_start: 0.7977 (tm-30) cc_final: 0.7709 (tm-30) REVERT: F 209 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7918 (mtm) REVERT: F 228 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8428 (ttpp) REVERT: H 122 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7485 (tm) REVERT: H 218 TYR cc_start: 0.8554 (t80) cc_final: 0.8301 (t80) REVERT: H 256 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7991 (mttt) REVERT: H 368 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6754 (pp20) REVERT: I 111 LEU cc_start: 0.7773 (mm) cc_final: 0.7547 (mm) REVERT: I 365 LYS cc_start: 0.8159 (mmtm) cc_final: 0.7725 (mmmm) REVERT: I 368 GLU cc_start: 0.7720 (pm20) cc_final: 0.7505 (pm20) REVERT: J 135 GLN cc_start: 0.7937 (mt0) cc_final: 0.7644 (mt0) REVERT: J 168 GLU cc_start: 0.7630 (tp30) cc_final: 0.7366 (mp0) REVERT: J 251 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7878 (m) REVERT: J 278 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7531 (mt) REVERT: K 18 ARG cc_start: 0.7306 (mpt180) cc_final: 0.6723 (mpt180) REVERT: K 103 MET cc_start: 0.6748 (mmt) cc_final: 0.5509 (mmt) REVERT: K 131 ASN cc_start: 0.8246 (OUTLIER) cc_final: 0.7921 (t0) REVERT: K 209 MET cc_start: 0.2107 (mmm) cc_final: 0.0351 (tmt) REVERT: K 368 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7035 (pp20) REVERT: G 1 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7247 (ppp) REVERT: G 342 LEU cc_start: 0.1816 (OUTLIER) cc_final: 0.1438 (mp) REVERT: G 345 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7748 (mtm110) REVERT: B 54 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.6069 (mp0) REVERT: B 63 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7250 (mp) REVERT: B 68 MET cc_start: 0.7469 (ttt) cc_final: 0.7198 (ttt) REVERT: B 78 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.7134 (mtt-85) REVERT: B 155 LEU cc_start: 0.8011 (tp) cc_final: 0.7780 (tt) outliers start: 112 outliers final: 59 residues processed: 482 average time/residue: 0.5825 time to fit residues: 319.1911 Evaluate side-chains 509 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 432 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 228 LYS Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 275 ASN Chi-restraints excluded: chain F residue 292 LYS Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 148 MET Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 256 LYS Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 91 LYS Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 208 SER Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 103 MET Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 145 CYS Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 299 GLN Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 353 LEU Chi-restraints excluded: chain K residue 361 ILE Chi-restraints excluded: chain K residue 368 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 172 GLN Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 247 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 19 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 234 optimal weight: 6.9990 chunk 37 optimal weight: 0.0370 chunk 224 optimal weight: 4.9990 chunk 203 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 168 optimal weight: 0.2980 chunk 94 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 82 GLN H 17 ASN H 86 ASN H 164 ASN I 17 ASN I 127 GLN I 135 GLN I 152 ASN I 306 ASN J 17 ASN J 69 GLN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.149067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.124924 restraints weight = 27839.406| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.16 r_work: 0.3534 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 19844 Z= 0.141 Angle : 0.578 9.337 27256 Z= 0.308 Chirality : 0.042 0.230 3067 Planarity : 0.004 0.112 3299 Dihedral : 16.720 141.735 3485 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.12 % Favored : 93.79 % Rotamer: Outliers : 5.09 % Allowed : 30.36 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.18), residues: 2288 helix: 1.31 (0.19), residues: 787 sheet: 0.68 (0.24), residues: 412 loop : -1.13 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 18 TYR 0.021 0.001 TYR I 265 PHE 0.021 0.001 PHE J 189 TRP 0.037 0.001 TRP B 59 HIS 0.003 0.001 HIS K 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (19844) covalent geometry : angle 0.57750 / 0.31 (27256) hydrogen bonds : bond 0.03492 / 3.54 ( 806) hydrogen bonds : angle 4.26736 / 4.51 ( 2299) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 433 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: F 52 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.7119 (m-80) REVERT: F 63 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7899 (mtt-85) REVERT: F 127 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7699 (tm-30) REVERT: F 209 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.7849 (mtm) REVERT: F 228 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8421 (ttpp) REVERT: H 122 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7452 (tm) REVERT: H 218 TYR cc_start: 0.8546 (t80) cc_final: 0.8301 (t80) REVERT: H 256 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8015 (mttt) REVERT: H 368 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6730 (pp20) REVERT: I 109 LYS cc_start: 0.7802 (tppp) cc_final: 0.7578 (tppp) REVERT: I 111 LEU cc_start: 0.7767 (mm) cc_final: 0.7544 (mm) REVERT: I 365 LYS cc_start: 0.8155 (mmtm) cc_final: 0.7703 (mmmm) REVERT: I 368 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7477 (pm20) REVERT: J 135 GLN cc_start: 0.7966 (mt0) cc_final: 0.7676 (mt0) REVERT: J 168 GLU cc_start: 0.7581 (tp30) cc_final: 0.7349 (mp0) REVERT: J 251 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7859 (m) REVERT: J 278 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7580 (mt) REVERT: K 18 ARG cc_start: 0.7300 (mpt180) cc_final: 0.6729 (mpt180) REVERT: K 32 VAL cc_start: 0.8187 (m) cc_final: 0.7756 (p) REVERT: K 103 MET cc_start: 0.6769 (mmt) cc_final: 0.5556 (mmt) REVERT: K 131 ASN cc_start: 0.8221 (t0) cc_final: 0.7899 (t0) REVERT: K 183 ARG cc_start: 0.7571 (mmm-85) cc_final: 0.7249 (mmm160) REVERT: K 209 MET cc_start: 0.2110 (mmm) cc_final: 0.0303 (tmt) REVERT: K 265 TYR cc_start: 0.6511 (OUTLIER) cc_final: 0.5125 (t80) REVERT: K 368 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7006 (pp20) REVERT: G 1 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7239 (ppp) REVERT: G 342 LEU cc_start: 0.1814 (OUTLIER) cc_final: 0.1450 (mp) REVERT: G 345 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7695 (mtm110) REVERT: B 54 GLU cc_start: 0.6314 (OUTLIER) cc_final: 0.6059 (mp0) REVERT: B 63 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7257 (mp) REVERT: B 68 MET cc_start: 0.7431 (ttt) cc_final: 0.7171 (ttt) REVERT: B 78 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6928 (mtt180) REVERT: B 155 LEU cc_start: 0.8036 (tp) cc_final: 0.7778 (tt) outliers start: 94 outliers final: 58 residues processed: 480 average time/residue: 0.5903 time to fit residues: 322.4362 Evaluate side-chains 503 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 427 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 228 LYS Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 292 LYS Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 256 LYS Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain I residue 91 LYS Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 208 SER Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain I residue 368 GLU Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 103 MET Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 145 CYS Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 265 TYR Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 299 GLN Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 353 LEU Chi-restraints excluded: chain K residue 361 ILE Chi-restraints excluded: chain K residue 368 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 172 GLN Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 247 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 37 optimal weight: 0.0030 chunk 180 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 232 optimal weight: 9.9990 chunk 130 optimal weight: 0.7980 chunk 162 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 217 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 17 ASN H 86 ASN H 164 ASN I 17 ASN I 127 GLN I 135 GLN I 152 ASN I 306 ASN J 17 ASN J 69 GLN J 86 ASN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 ASN ** K 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.148712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.124741 restraints weight = 27610.115| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.14 r_work: 0.3529 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 19844 Z= 0.152 Angle : 0.586 9.912 27256 Z= 0.310 Chirality : 0.043 0.236 3067 Planarity : 0.004 0.112 3299 Dihedral : 16.724 143.635 3484 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.08 % Favored : 93.84 % Rotamer: Outliers : 4.98 % Allowed : 30.63 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.18), residues: 2288 helix: 1.30 (0.19), residues: 788 sheet: 0.65 (0.24), residues: 413 loop : -1.12 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 286 TYR 0.023 0.001 TYR I 265 PHE 0.021 0.001 PHE J 189 TRP 0.055 0.002 TRP F 78 HIS 0.003 0.001 HIS K 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (19844) covalent geometry : angle 0.58554 / 0.31 (27256) hydrogen bonds : bond 0.03519 / 3.56 ( 806) hydrogen bonds : angle 4.24854 / 4.51 ( 2299) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 436 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 52 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7120 (m-80) REVERT: F 63 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7897 (mtt-85) REVERT: F 103 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.6402 (pp-130) REVERT: F 127 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7691 (tm-30) REVERT: F 209 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.7834 (mtm) REVERT: F 228 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8427 (ttpp) REVERT: H 122 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7508 (tm) REVERT: H 218 TYR cc_start: 0.8551 (t80) cc_final: 0.8302 (t80) REVERT: H 256 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8022 (mttt) REVERT: H 368 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6720 (pp20) REVERT: I 111 LEU cc_start: 0.7788 (mm) cc_final: 0.7566 (mm) REVERT: J 135 GLN cc_start: 0.7973 (mt0) cc_final: 0.7690 (mt0) REVERT: J 168 GLU cc_start: 0.7582 (tp30) cc_final: 0.7355 (mp0) REVERT: J 251 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7856 (m) REVERT: J 278 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7564 (mt) REVERT: K 18 ARG cc_start: 0.7302 (mpt180) cc_final: 0.6797 (mpt180) REVERT: K 32 VAL cc_start: 0.8179 (m) cc_final: 0.7751 (p) REVERT: K 103 MET cc_start: 0.6800 (mmt) cc_final: 0.5532 (mmt) REVERT: K 131 ASN cc_start: 0.8228 (t0) cc_final: 0.7856 (t0) REVERT: K 183 ARG cc_start: 0.7572 (mmm-85) cc_final: 0.7254 (mmm160) REVERT: K 209 MET cc_start: 0.2082 (mmm) cc_final: 0.0271 (tmt) REVERT: K 368 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7014 (pp20) REVERT: G 1 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7251 (ppp) REVERT: G 342 LEU cc_start: 0.1864 (OUTLIER) cc_final: 0.1496 (mp) REVERT: G 345 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7698 (mtm110) REVERT: B 54 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.6062 (mp0) REVERT: B 68 MET cc_start: 0.7408 (ttt) cc_final: 0.7149 (ttt) outliers start: 92 outliers final: 58 residues processed: 481 average time/residue: 0.5871 time to fit residues: 320.6469 Evaluate side-chains 507 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 434 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 228 LYS Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 292 LYS Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 256 LYS Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 91 LYS Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 208 SER Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 103 MET Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 145 CYS Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 299 GLN Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 361 ILE Chi-restraints excluded: chain K residue 368 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 172 GLN Chi-restraints excluded: chain G residue 221 ILE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 247 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 179 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 210 optimal weight: 9.9990 chunk 71 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 225 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 134 optimal weight: 4.9990 chunk 14 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 17 ASN H 86 ASN H 164 ASN I 17 ASN I 127 GLN I 152 ASN I 306 ASN I 349 ASN J 17 ASN J 69 GLN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 ASN K 131 ASN ** K 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.148536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.124567 restraints weight = 27851.140| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.15 r_work: 0.3526 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 19844 Z= 0.152 Angle : 0.588 9.036 27256 Z= 0.312 Chirality : 0.043 0.236 3067 Planarity : 0.004 0.112 3299 Dihedral : 16.714 145.598 3484 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.94 % Favored : 93.97 % Rotamer: Outliers : 4.49 % Allowed : 31.55 % Favored : 63.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.18), residues: 2288 helix: 1.30 (0.19), residues: 787 sheet: 0.66 (0.24), residues: 413 loop : -1.13 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 286 TYR 0.025 0.001 TYR I 265 PHE 0.021 0.001 PHE J 189 TRP 0.084 0.002 TRP F 78 HIS 0.003 0.001 HIS K 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (19844) covalent geometry : angle 0.58821 / 0.31 (27256) hydrogen bonds : bond 0.03538 / 3.59 ( 806) hydrogen bonds : angle 4.23993 / 4.50 ( 2299) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 427 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: F 52 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.7130 (m-80) REVERT: F 63 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7928 (mtt-85) REVERT: F 78 TRP cc_start: 0.8052 (t60) cc_final: 0.7775 (t60) REVERT: F 103 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.6443 (pp-130) REVERT: F 107 LYS cc_start: 0.7553 (tppp) cc_final: 0.7055 (tppp) REVERT: F 127 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7687 (tm-30) REVERT: F 209 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.7848 (mtm) REVERT: F 323 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7792 (mp) REVERT: H 122 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7499 (tm) REVERT: H 218 TYR cc_start: 0.8553 (t80) cc_final: 0.8306 (t80) REVERT: H 256 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8025 (mttt) REVERT: H 368 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6728 (pp20) REVERT: I 111 LEU cc_start: 0.7796 (mm) cc_final: 0.7577 (mm) REVERT: J 135 GLN cc_start: 0.7969 (mt0) cc_final: 0.7685 (mt0) REVERT: J 168 GLU cc_start: 0.7570 (tp30) cc_final: 0.7344 (mp0) REVERT: J 251 THR cc_start: 0.8132 (OUTLIER) cc_final: 0.7872 (m) REVERT: J 278 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7538 (mt) REVERT: K 18 ARG cc_start: 0.7306 (mpt180) cc_final: 0.6812 (mpt180) REVERT: K 32 VAL cc_start: 0.8183 (m) cc_final: 0.7756 (p) REVERT: K 103 MET cc_start: 0.6829 (mmt) cc_final: 0.5516 (mmt) REVERT: K 131 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.7915 (t0) REVERT: K 183 ARG cc_start: 0.7586 (mmm-85) cc_final: 0.7291 (mmm160) REVERT: K 209 MET cc_start: 0.2067 (mmm) cc_final: 0.0250 (tmt) REVERT: K 368 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7047 (pp20) REVERT: G 1 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7232 (ppp) REVERT: G 209 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7974 (mmm) REVERT: G 342 LEU cc_start: 0.1932 (OUTLIER) cc_final: 0.1557 (mp) REVERT: G 345 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7700 (mtm110) REVERT: B 54 GLU cc_start: 0.6336 (OUTLIER) cc_final: 0.6088 (mp0) REVERT: B 68 MET cc_start: 0.7403 (ttt) cc_final: 0.7143 (ttt) outliers start: 83 outliers final: 59 residues processed: 469 average time/residue: 0.5666 time to fit residues: 302.0434 Evaluate side-chains 503 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 427 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 292 LYS Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 256 LYS Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 91 LYS Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 152 ASN Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 103 MET Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 145 CYS Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 299 GLN Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 361 ILE Chi-restraints excluded: chain K residue 368 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 172 GLN Chi-restraints excluded: chain G residue 209 MET Chi-restraints excluded: chain G residue 221 ILE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 247 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 147 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 80 optimal weight: 0.0980 chunk 221 optimal weight: 0.9980 chunk 208 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 218 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 17 ASN H 86 ASN H 164 ASN ** H 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 127 GLN I 152 ASN I 306 ASN J 17 ASN J 69 GLN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 131 ASN ** K 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.148500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.124546 restraints weight = 27745.963| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.15 r_work: 0.3527 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.188 19844 Z= 0.194 Angle : 0.781 59.116 27256 Z= 0.450 Chirality : 0.043 0.238 3067 Planarity : 0.005 0.124 3299 Dihedral : 16.716 145.600 3484 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.94 % Favored : 93.97 % Rotamer: Outliers : 4.49 % Allowed : 31.44 % Favored : 64.07 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.18), residues: 2288 helix: 1.27 (0.19), residues: 788 sheet: 0.66 (0.24), residues: 413 loop : -1.12 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 286 TYR 0.022 0.001 TYR I 265 PHE 0.018 0.001 PHE J 189 TRP 0.077 0.002 TRP F 78 HIS 0.003 0.001 HIS K 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (19844) covalent geometry : angle 0.78055 / 0.45 (27256) hydrogen bonds : bond 0.03544 / 3.59 ( 806) hydrogen bonds : angle 4.24441 / 4.51 ( 2299) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8372.69 seconds wall clock time: 143 minutes 12.98 seconds (8592.98 seconds total)