Starting phenix.real_space_refine on Fri Aug 7 04:32:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zp9_60330/08_2026/8zp9_60330.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zp9_60330/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zp9_60330/08_2026/8zp9_60330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zp9_60330/08_2026/8zp9_60330.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zp9_60330/08_2026/8zp9_60330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zp9_60330/08_2026/8zp9_60330.map" } 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-2.2rc3-6140/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: 4.34, 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: 1.71 Conformation dependent library (CDL) restraints added in 668.5 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: 2.56 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: 3.85 Time building geometry restraints manager: 2.20 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: 26868 2.39 - 4.79: 340 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: 2459 0.051 - 0.103: 491 0.103 - 0.154: 111 0.154 - 0.205: 4 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: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.930 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:8.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.150 ------------------------------------------------------------------------------- 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= 0.211 Angle : 0.659 11.975 27256 Z= 0.427 Chirality : 0.044 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 0.00357 / 0.21 (19844) covalent geometry : angle 0.65881 / 0.43 (27256) hydrogen bonds : bond 0.18395 / 20.27 ( 806) hydrogen bonds : angle 6.50419 / 6.65 ( 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: 0.5869 time to fit residues: 315.5928 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 : 0.673 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.8884 ------------------------------------------------------------------------------- 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.153384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.128997 restraints weight = 27943.395| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.18 r_work: 0.3590 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.0826 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= 0.185 Angle : 0.620 11.054 27256 Z= 0.333 Chirality : 0.044 0.255 3067 Planarity : 0.005 0.115 3299 Dihedral : 16.938 139.767 3539 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.08 % Favored : 93.84 % 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: 0.22 (0.18), residues: 2288 helix: 1.23 (0.19), residues: 784 sheet: 1.24 (0.24), residues: 398 loop : -1.10 (0.19), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 286 TYR 0.018 0.001 TYR I 265 PHE 0.014 0.002 PHE J 189 TRP 0.021 0.001 TRP B 59 HIS 0.003 0.001 HIS F 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (19844) covalent geometry : angle 0.61989 / 0.33 (27256) hydrogen bonds : bond 0.04740 / 5.15 ( 806) hydrogen bonds : angle 4.83481 / 5.15 ( 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 541 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 447 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: F 63 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7803 (mtt-85) REVERT: F 103 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.6433 (pp-130) REVERT: F 127 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7488 (tm-30) REVERT: F 209 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7835 (mtm) REVERT: F 250 LYS cc_start: 0.8545 (mtmm) cc_final: 0.8333 (mtmm) REVERT: F 278 ILE cc_start: 0.8392 (mm) cc_final: 0.8145 (mt) REVERT: H 209 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7676 (mtm) REVERT: H 218 TYR cc_start: 0.8650 (t80) cc_final: 0.8178 (t80) REVERT: H 256 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8100 (mttt) REVERT: H 368 GLU cc_start: 0.6923 (pp20) cc_final: 0.6620 (pp20) REVERT: I 111 LEU cc_start: 0.7758 (mm) cc_final: 0.7501 (mm) REVERT: I 150 GLU cc_start: 0.7537 (mp0) cc_final: 0.7012 (tt0) REVERT: I 209 MET cc_start: 0.8135 (mtm) cc_final: 0.7884 (mpp) REVERT: J 86 ASN cc_start: 0.8137 (m-40) cc_final: 0.7896 (m110) REVERT: J 168 GLU cc_start: 0.7508 (tp30) cc_final: 0.7221 (mp0) REVERT: J 274 LYS cc_start: 0.7475 (ptpt) cc_final: 0.7167 (pttt) REVERT: J 330 ASN cc_start: 0.7954 (t0) cc_final: 0.7629 (t0) REVERT: K 18 ARG cc_start: 0.7294 (mpt180) cc_final: 0.6896 (mpt180) REVERT: K 131 ASN cc_start: 0.8007 (t0) cc_final: 0.7577 (t0) REVERT: K 209 MET cc_start: 0.2448 (mmm) cc_final: 0.0979 (tmt) REVERT: K 338 LYS cc_start: -0.0700 (OUTLIER) cc_final: -0.1189 (mttp) REVERT: B 68 MET cc_start: 0.7458 (ttt) cc_final: 0.7204 (ttt) outliers start: 94 outliers final: 48 residues processed: 500 average time/residue: 0.5880 time to fit residues: 333.5974 Evaluate side-chains 490 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 436 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 VAL 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 293 GLU Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain H residue 64 LEU 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 161 LYS 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 J residue 352 GLU Chi-restraints excluded: chain K residue 297 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 46 ILE Chi-restraints excluded: chain G residue 172 GLN 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: 1.9990 chunk 141 optimal weight: 4.9990 chunk 201 optimal weight: 0.0670 chunk 53 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 212 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN H 164 ASN I 17 ASN I 82 GLN I 92 ASN I 127 GLN J 17 ASN J 69 GLN J 204 HIS ** 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 349 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.152907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.128356 restraints weight = 28094.313| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.19 r_work: 0.3552 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 19844 Z= 0.187 Angle : 0.605 10.204 27256 Z= 0.325 Chirality : 0.044 0.256 3067 Planarity : 0.005 0.115 3299 Dihedral : 16.804 142.418 3506 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.03 % Favored : 93.88 % Rotamer: Outliers : 6.71 % Allowed : 28.19 % 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: 0.11 (0.18), residues: 2288 helix: 1.18 (0.19), residues: 786 sheet: 0.99 (0.24), residues: 406 loop : -1.14 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 286 TYR 0.018 0.001 TYR I 265 PHE 0.020 0.001 PHE J 189 TRP 0.038 0.001 TRP B 59 HIS 0.007 0.001 HIS K 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 (19844) covalent geometry : angle 0.60469 / 0.32 (27256) hydrogen bonds : bond 0.04187 / 4.56 ( 806) hydrogen bonds : angle 4.53644 / 4.93 ( 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 578 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 454 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: F 52 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7331 (m-80) REVERT: F 63 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7832 (mtt-85) REVERT: F 103 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.6505 (pp-130) REVERT: F 107 LYS cc_start: 0.7346 (tppp) cc_final: 0.6828 (tppp) REVERT: F 127 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7633 (tm-30) REVERT: F 209 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7901 (mtm) REVERT: F 278 ILE cc_start: 0.8437 (mm) cc_final: 0.8232 (mt) REVERT: H 122 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7633 (tm) REVERT: H 256 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8057 (mttt) REVERT: H 368 GLU cc_start: 0.6994 (pp20) cc_final: 0.6674 (pp20) REVERT: I 111 LEU cc_start: 0.7810 (mm) cc_final: 0.7560 (mm) REVERT: I 150 GLU cc_start: 0.7365 (mp0) cc_final: 0.6984 (tt0) REVERT: J 135 GLN cc_start: 0.7827 (mt0) cc_final: 0.7598 (mt0) REVERT: J 168 GLU cc_start: 0.7619 (tp30) cc_final: 0.7337 (mp0) REVERT: J 251 THR cc_start: 0.8130 (OUTLIER) cc_final: 0.7877 (m) REVERT: J 272 GLU cc_start: 0.7452 (pt0) cc_final: 0.7073 (pt0) REVERT: J 274 LYS cc_start: 0.7504 (ptpt) cc_final: 0.7285 (pttt) REVERT: J 278 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7550 (mt) REVERT: K 18 ARG cc_start: 0.7339 (mpt180) cc_final: 0.7032 (mpt180) REVERT: K 103 MET cc_start: 0.6722 (mmt) cc_final: 0.5621 (mmt) REVERT: K 131 ASN cc_start: 0.8118 (OUTLIER) cc_final: 0.7754 (t0) REVERT: K 209 MET cc_start: 0.2473 (mmm) cc_final: 0.0825 (tmt) REVERT: G 345 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7682 (mtm110) REVERT: B 68 MET cc_start: 0.7505 (ttt) cc_final: 0.7235 (ttt) outliers start: 124 outliers final: 54 residues processed: 515 average time/residue: 0.5791 time to fit residues: 339.3316 Evaluate side-chains 490 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 426 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 ASP 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 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 45 SER 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 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 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 J residue 352 GLU Chi-restraints excluded: chain K residue 131 ASN 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 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 345 ARG Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 191 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 101 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 20 optimal weight: 0.0670 chunk 93 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 202 optimal weight: 0.0770 chunk 156 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN H 86 ASN H 164 ASN I 17 ASN I 127 GLN I 306 ASN J 17 ASN J 69 GLN J 86 ASN J 225 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 303 GLN K 349 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.150217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.125737 restraints weight = 27902.966| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.19 r_work: 0.3542 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 19844 Z= 0.189 Angle : 0.608 10.789 27256 Z= 0.324 Chirality : 0.044 0.231 3067 Planarity : 0.004 0.115 3299 Dihedral : 16.751 143.236 3490 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.86 % Favored : 94.06 % Rotamer: Outliers : 5.79 % Allowed : 29.55 % Favored : 64.66 % 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: 0.06 (0.18), residues: 2288 helix: 1.18 (0.19), residues: 787 sheet: 0.89 (0.24), residues: 404 loop : -1.17 (0.19), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 286 TYR 0.020 0.001 TYR I 265 PHE 0.020 0.001 PHE J 189 TRP 0.029 0.001 TRP B 59 HIS 0.005 0.001 HIS K 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (19844) covalent geometry : angle 0.60801 / 0.32 (27256) hydrogen bonds : bond 0.03907 / 4.24 ( 806) hydrogen bonds : angle 4.45504 / 4.84 ( 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 534 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 427 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 52 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7139 (m-80) REVERT: F 63 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7913 (mtt-85) REVERT: F 103 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.6460 (pp-130) REVERT: F 107 LYS cc_start: 0.7373 (tppp) cc_final: 0.6786 (tppp) REVERT: F 127 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7634 (tm-30) REVERT: F 147 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7739 (ptt90) REVERT: F 209 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7879 (mtm) REVERT: H 122 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7581 (tm) REVERT: H 218 TYR cc_start: 0.8551 (t80) cc_final: 0.8237 (t80) REVERT: H 256 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8021 (mttt) REVERT: H 368 GLU cc_start: 0.6992 (pp20) cc_final: 0.6667 (pp20) REVERT: I 111 LEU cc_start: 0.7780 (mm) cc_final: 0.7526 (mm) REVERT: I 150 GLU cc_start: 0.7235 (mp0) cc_final: 0.6957 (tt0) REVERT: I 365 LYS cc_start: 0.8068 (mmtm) cc_final: 0.7759 (mtpp) REVERT: J 135 GLN cc_start: 0.7966 (mt0) cc_final: 0.7702 (mt0) REVERT: J 168 GLU cc_start: 0.7620 (tp30) cc_final: 0.7351 (mp0) REVERT: J 251 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7889 (m) REVERT: J 272 GLU cc_start: 0.7448 (pt0) cc_final: 0.6986 (pt0) REVERT: J 274 LYS cc_start: 0.7651 (ptpt) cc_final: 0.7206 (pttt) REVERT: J 278 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7519 (mt) REVERT: K 18 ARG cc_start: 0.7362 (mpt180) cc_final: 0.6825 (mpt180) REVERT: K 103 MET cc_start: 0.6804 (mmt) cc_final: 0.5600 (mmt) REVERT: K 131 ASN cc_start: 0.8217 (OUTLIER) cc_final: 0.7939 (t0) REVERT: K 246 LEU cc_start: 0.8387 (mm) cc_final: 0.8032 (mp) REVERT: K 368 GLU cc_start: 0.7438 (pp20) cc_final: 0.6948 (pp20) REVERT: G 1 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7276 (ppp) REVERT: G 342 LEU cc_start: 0.1561 (OUTLIER) cc_final: 0.1201 (mp) REVERT: G 345 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7689 (mtm110) REVERT: B 63 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7427 (mt) REVERT: B 68 MET cc_start: 0.7517 (ttt) cc_final: 0.7237 (ttt) outliers start: 107 outliers final: 59 residues processed: 482 average time/residue: 0.5933 time to fit residues: 325.0772 Evaluate side-chains 496 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 423 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 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 190 VAL 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 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 250 LYS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain J residue 352 GLU 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 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 342 LEU Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 191 SER 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: 0.8980 chunk 232 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 184 optimal weight: 4.9990 chunk 197 optimal weight: 0.9990 chunk 92 optimal weight: 0.0040 chunk 83 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 180 HIS 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 ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 ASN K 131 ASN K 229 ASN K 349 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.150295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.126021 restraints weight = 27941.698| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.17 r_work: 0.3545 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 19844 Z= 0.158 Angle : 0.583 9.858 27256 Z= 0.312 Chirality : 0.043 0.228 3067 Planarity : 0.004 0.114 3299 Dihedral : 16.737 144.254 3490 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.99 % Favored : 93.92 % Rotamer: Outliers : 5.52 % Allowed : 29.11 % Favored : 65.37 % 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: 0.08 (0.18), residues: 2288 helix: 1.23 (0.19), residues: 787 sheet: 0.82 (0.24), residues: 406 loop : -1.16 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 18 TYR 0.019 0.001 TYR I 265 PHE 0.019 0.001 PHE J 189 TRP 0.025 0.001 TRP B 59 HIS 0.005 0.001 HIS K 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (19844) covalent geometry : angle 0.58313 / 0.31 (27256) hydrogen bonds : bond 0.03725 / 4.09 ( 806) hydrogen bonds : angle 4.37557 / 4.77 ( 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 526 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 424 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 52 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7063 (m-80) REVERT: F 63 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7841 (mtt-85) REVERT: F 103 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.6557 (pp-130) REVERT: F 107 LYS cc_start: 0.7340 (tppp) cc_final: 0.6724 (tppp) REVERT: F 127 GLN cc_start: 0.7931 (mm-40) cc_final: 0.7657 (tm-30) REVERT: F 209 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7907 (mtm) REVERT: H 122 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7532 (tm) REVERT: H 256 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8008 (mttt) REVERT: H 365 LYS cc_start: 0.8168 (mppt) cc_final: 0.7244 (mppt) REVERT: H 368 GLU cc_start: 0.6995 (pp20) cc_final: 0.6584 (pp20) REVERT: I 1 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8223 (ptm) REVERT: I 111 LEU cc_start: 0.7779 (mm) cc_final: 0.7534 (mm) REVERT: I 148 MET cc_start: 0.8392 (tmt) cc_final: 0.8042 (tmt) REVERT: I 365 LYS cc_start: 0.8083 (mmtm) cc_final: 0.7856 (mtpp) REVERT: J 44 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8252 (tpt170) REVERT: J 135 GLN cc_start: 0.7940 (mt0) cc_final: 0.7658 (mt0) REVERT: J 168 GLU cc_start: 0.7622 (tp30) cc_final: 0.7360 (mp0) REVERT: J 251 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7877 (m) REVERT: J 278 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7491 (mt) REVERT: K 18 ARG cc_start: 0.7355 (mpt180) cc_final: 0.6880 (mpt180) REVERT: K 35 SER cc_start: 0.8391 (OUTLIER) cc_final: 0.8112 (m) REVERT: K 103 MET cc_start: 0.6735 (mmt) cc_final: 0.5518 (mmt) REVERT: K 131 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.8001 (t0) REVERT: K 209 MET cc_start: 0.2338 (mmm) cc_final: 0.0574 (tmt) REVERT: K 368 GLU cc_start: 0.7469 (pp20) cc_final: 0.6984 (pp20) REVERT: G 1 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7251 (ppp) REVERT: G 342 LEU cc_start: 0.1602 (OUTLIER) cc_final: 0.1234 (mp) REVERT: B 54 GLU cc_start: 0.6311 (OUTLIER) cc_final: 0.6052 (mp0) REVERT: B 68 MET cc_start: 0.7475 (ttt) cc_final: 0.7185 (ttt) outliers start: 102 outliers final: 59 residues processed: 480 average time/residue: 0.5871 time to fit residues: 319.1250 Evaluate side-chains 497 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 423 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 20 ASP 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 62 ARG 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 114 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 167 VAL 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 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 234 THR Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain J residue 44 ARG 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 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 J residue 352 GLU Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 88 CYS 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 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 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 247 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 82 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 208 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 J 17 ASN J 69 GLN J 86 ASN J 127 GLN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 131 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.148020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.123577 restraints weight = 27658.303| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.18 r_work: 0.3513 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1915 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= 0.230 Angle : 0.621 11.129 27256 Z= 0.331 Chirality : 0.045 0.258 3067 Planarity : 0.004 0.115 3299 Dihedral : 16.818 145.065 3490 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.16 % Favored : 93.75 % Rotamer: Outliers : 6.11 % Allowed : 28.46 % Favored : 65.42 % 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: -0.05 (0.18), residues: 2288 helix: 1.14 (0.19), residues: 782 sheet: 0.68 (0.24), residues: 408 loop : -1.21 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 286 TYR 0.021 0.001 TYR I 265 PHE 0.024 0.002 PHE J 189 TRP 0.029 0.002 TRP B 59 HIS 0.005 0.001 HIS K 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.23 (19844) covalent geometry : angle 0.62098 / 0.33 (27256) hydrogen bonds : bond 0.03980 / 4.35 ( 806) hydrogen bonds : angle 4.43967 / 4.85 ( 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 533 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 420 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 52 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7148 (m-80) REVERT: F 63 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7980 (mtt-85) REVERT: F 103 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.6473 (pp-130) REVERT: F 107 LYS cc_start: 0.7406 (tppp) cc_final: 0.6791 (tppp) REVERT: F 127 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7750 (tm-30) REVERT: F 209 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7888 (mtm) REVERT: H 122 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7526 (tm) REVERT: H 218 TYR cc_start: 0.8557 (t80) cc_final: 0.8330 (t80) REVERT: H 365 LYS cc_start: 0.8211 (mppt) cc_final: 0.7800 (mppt) REVERT: H 370 GLN cc_start: 0.7234 (mt0) cc_final: 0.6915 (mt0) REVERT: I 1 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8192 (ptm) REVERT: I 111 LEU cc_start: 0.7822 (mm) cc_final: 0.7603 (mm) REVERT: I 365 LYS cc_start: 0.8110 (mmtm) cc_final: 0.7900 (mtpp) REVERT: J 44 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8261 (tpt170) REVERT: J 135 GLN cc_start: 0.7940 (mt0) cc_final: 0.7686 (mt0) REVERT: J 168 GLU cc_start: 0.7629 (tp30) cc_final: 0.7364 (mp0) REVERT: K 18 ARG cc_start: 0.7416 (mpt180) cc_final: 0.7058 (mpt180) REVERT: K 35 SER cc_start: 0.8385 (OUTLIER) cc_final: 0.8158 (m) REVERT: K 103 MET cc_start: 0.6985 (mmt) cc_final: 0.5629 (mmt) REVERT: K 131 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7952 (t0) REVERT: K 209 MET cc_start: 0.2284 (mmm) cc_final: 0.0437 (tmt) REVERT: K 286 ARG cc_start: 0.8475 (mmm160) cc_final: 0.8233 (mmm160) REVERT: K 368 GLU cc_start: 0.7495 (pp20) cc_final: 0.7014 (pp20) REVERT: G 1 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7239 (ppp) REVERT: G 342 LEU cc_start: 0.1673 (OUTLIER) cc_final: 0.1352 (mp) REVERT: B 54 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.6116 (mp0) REVERT: B 68 MET cc_start: 0.7538 (ttt) cc_final: 0.7276 (ttt) outliers start: 113 outliers final: 70 residues processed: 477 average time/residue: 0.5752 time to fit residues: 311.1036 Evaluate side-chains 508 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 426 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 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 64 LEU 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 190 VAL 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 45 SER 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 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 I residue 320 SER Chi-restraints excluded: chain J residue 44 ARG 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 352 GLU Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 56 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 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 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 212 SER 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 44 LEU 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 164 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 82 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 chunk 202 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 148 optimal weight: 0.9980 chunk 174 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 J 17 ASN J 69 GLN J 127 GLN J 349 ASN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 131 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.149196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.125014 restraints weight = 27734.524| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.16 r_work: 0.3532 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1970 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= 0.150 Angle : 0.581 9.656 27256 Z= 0.311 Chirality : 0.042 0.219 3067 Planarity : 0.004 0.114 3299 Dihedral : 16.767 146.076 3488 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.08 % Favored : 93.84 % Rotamer: Outliers : 5.52 % Allowed : 29.38 % 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: 0.06 (0.18), residues: 2288 helix: 1.26 (0.19), residues: 786 sheet: 0.72 (0.24), residues: 407 loop : -1.16 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 18 TYR 0.024 0.001 TYR I 265 PHE 0.022 0.001 PHE J 189 TRP 0.033 0.001 TRP B 59 HIS 0.004 0.001 HIS K 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (19844) covalent geometry : angle 0.58096 / 0.31 (27256) hydrogen bonds : bond 0.03602 / 3.94 ( 806) hydrogen bonds : angle 4.33299 / 4.74 ( 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 531 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 429 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 52 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.7107 (m-80) REVERT: F 63 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7844 (mtt-85) REVERT: F 107 LYS cc_start: 0.7387 (tppp) cc_final: 0.6772 (tppp) REVERT: F 127 GLN cc_start: 0.7968 (mm-40) cc_final: 0.7672 (tm-30) REVERT: F 209 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7902 (mtm) REVERT: H 122 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7515 (tm) REVERT: H 218 TYR cc_start: 0.8558 (t80) cc_final: 0.8286 (t80) REVERT: H 256 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7996 (mttt) REVERT: H 365 LYS cc_start: 0.8196 (mppt) cc_final: 0.7799 (mppt) REVERT: I 111 LEU cc_start: 0.7807 (mm) cc_final: 0.7584 (mm) REVERT: J 135 GLN cc_start: 0.7909 (mt0) cc_final: 0.7627 (mt0) REVERT: J 168 GLU cc_start: 0.7622 (tp30) cc_final: 0.7363 (mp0) REVERT: K 18 ARG cc_start: 0.7344 (mpt180) cc_final: 0.6895 (mpt180) REVERT: K 103 MET cc_start: 0.6838 (mmt) cc_final: 0.5555 (mmt) REVERT: K 131 ASN cc_start: 0.8193 (OUTLIER) cc_final: 0.7963 (t0) REVERT: K 209 MET cc_start: 0.2115 (mmm) cc_final: 0.0336 (tmt) REVERT: K 286 ARG cc_start: 0.8473 (mmm160) cc_final: 0.8231 (mmm160) REVERT: K 368 GLU cc_start: 0.7522 (pp20) cc_final: 0.7035 (pp20) REVERT: G 1 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7232 (ppp) REVERT: G 34 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7018 (mtt180) REVERT: G 342 LEU cc_start: 0.1664 (OUTLIER) cc_final: 0.1327 (mp) REVERT: G 345 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7726 (mtm110) REVERT: B 54 GLU cc_start: 0.6331 (OUTLIER) cc_final: 0.6073 (mp0) REVERT: B 68 MET cc_start: 0.7465 (ttt) cc_final: 0.7209 (ttt) REVERT: B 78 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.7137 (mtt-85) REVERT: B 155 LEU cc_start: 0.8000 (tp) cc_final: 0.7783 (tt) outliers start: 102 outliers final: 61 residues processed: 485 average time/residue: 0.5391 time to fit residues: 296.6867 Evaluate side-chains 491 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 418 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 163 SER 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 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 116 LEU 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 320 SER 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 352 GLU Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 131 ASN 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 34 ARG 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 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 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 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 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: 2.9990 chunk 234 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 224 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 168 optimal weight: 0.0060 chunk 94 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 170 optimal weight: 0.8980 overall best weight: 0.9798 ------------------------------------------------------------------------------- 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 349 ASN J 17 ASN J 69 GLN J 86 ASN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 131 ASN K 349 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.147514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.123366 restraints weight = 27731.513| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.16 r_work: 0.3510 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 19844 Z= 0.192 Angle : 0.606 9.657 27256 Z= 0.323 Chirality : 0.044 0.230 3067 Planarity : 0.004 0.113 3299 Dihedral : 16.801 148.827 3486 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.16 % Favored : 93.75 % Rotamer: Outliers : 5.30 % Allowed : 29.49 % Favored : 65.21 % 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: 1.23 (0.19), residues: 780 sheet: 0.66 (0.24), residues: 408 loop : -1.17 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 286 TYR 0.029 0.001 TYR I 265 PHE 0.025 0.001 PHE J 189 TRP 0.038 0.001 TRP B 59 HIS 0.004 0.001 HIS K 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (19844) covalent geometry : angle 0.60648 / 0.32 (27256) hydrogen bonds : bond 0.03787 / 4.15 ( 806) hydrogen bonds : angle 4.35665 / 4.76 ( 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 522 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 424 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: F 52 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7105 (m-80) REVERT: F 63 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7953 (mtt-85) REVERT: F 127 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7736 (tm-30) REVERT: F 209 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7854 (mtm) REVERT: F 228 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8388 (ttpp) REVERT: H 122 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7475 (tm) REVERT: H 218 TYR cc_start: 0.8568 (t80) cc_final: 0.8311 (t80) REVERT: H 365 LYS cc_start: 0.8213 (mppt) cc_final: 0.7804 (mppt) REVERT: H 370 GLN cc_start: 0.7358 (mt0) cc_final: 0.7148 (mt0) REVERT: I 111 LEU cc_start: 0.7826 (mm) cc_final: 0.7611 (mm) REVERT: J 135 GLN cc_start: 0.7951 (mt0) cc_final: 0.7662 (mt0) REVERT: J 168 GLU cc_start: 0.7559 (tp30) cc_final: 0.7309 (mp0) REVERT: K 18 ARG cc_start: 0.7446 (mpt180) cc_final: 0.7135 (mpt180) REVERT: K 103 MET cc_start: 0.7041 (mmt) cc_final: 0.5694 (mmt) REVERT: K 131 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7895 (t0) REVERT: K 183 ARG cc_start: 0.7599 (mmm-85) cc_final: 0.7280 (mmm160) REVERT: K 286 ARG cc_start: 0.8483 (mmm160) cc_final: 0.8242 (mmm160) REVERT: K 368 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7050 (pp20) REVERT: G 1 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7245 (ppp) REVERT: G 34 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.6702 (mtt180) REVERT: G 342 LEU cc_start: 0.1926 (OUTLIER) cc_final: 0.1610 (mp) REVERT: B 54 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.6114 (mp0) REVERT: B 63 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7255 (mp) REVERT: B 68 MET cc_start: 0.7468 (ttt) cc_final: 0.7215 (ttt) REVERT: B 155 LEU cc_start: 0.8126 (tp) cc_final: 0.7870 (tt) outliers start: 98 outliers final: 66 residues processed: 472 average time/residue: 0.5521 time to fit residues: 296.3336 Evaluate side-chains 500 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 422 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 ASP 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 163 SER 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 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 190 VAL 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 320 SER 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 298 GLU Chi-restraints excluded: chain J residue 352 GLU Chi-restraints excluded: chain K residue 56 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 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 34 ARG 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 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 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 247 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 37 optimal weight: 0.5980 chunk 180 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 232 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 217 optimal weight: 0.0980 chunk 48 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 J 17 ASN J 69 GLN J 349 ASN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.148140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.124193 restraints weight = 27591.254| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.14 r_work: 0.3522 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 19844 Z= 0.155 Angle : 0.598 10.154 27256 Z= 0.317 Chirality : 0.042 0.220 3067 Planarity : 0.004 0.113 3299 Dihedral : 16.772 150.200 3486 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.12 % Favored : 93.79 % Rotamer: Outliers : 5.03 % Allowed : 30.36 % Favored : 64.61 % 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: 0.06 (0.18), residues: 2288 helix: 1.30 (0.19), residues: 780 sheet: 0.65 (0.24), residues: 411 loop : -1.15 (0.19), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 286 TYR 0.034 0.001 TYR I 265 PHE 0.022 0.001 PHE J 189 TRP 0.052 0.002 TRP F 78 HIS 0.004 0.001 HIS K 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (19844) covalent geometry : angle 0.59820 / 0.32 (27256) hydrogen bonds : bond 0.03613 / 3.98 ( 806) hydrogen bonds : angle 4.29575 / 4.70 ( 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 508 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 415 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 52 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7080 (m-80) REVERT: F 63 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7901 (mtt-85) REVERT: F 209 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7843 (mtm) REVERT: F 310 ASP cc_start: 0.8081 (m-30) cc_final: 0.7871 (m-30) REVERT: H 122 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7475 (tm) REVERT: H 218 TYR cc_start: 0.8569 (t80) cc_final: 0.8316 (t80) REVERT: H 256 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8008 (mttt) REVERT: H 365 LYS cc_start: 0.8189 (mppt) cc_final: 0.7786 (mppt) REVERT: H 370 GLN cc_start: 0.7355 (mt0) cc_final: 0.7126 (mt0) REVERT: I 111 LEU cc_start: 0.7811 (mm) cc_final: 0.7602 (mm) REVERT: J 135 GLN cc_start: 0.7941 (mt0) cc_final: 0.7675 (mt0) REVERT: J 168 GLU cc_start: 0.7551 (tp30) cc_final: 0.7324 (mp0) REVERT: J 251 THR cc_start: 0.8128 (OUTLIER) cc_final: 0.7884 (m) REVERT: K 18 ARG cc_start: 0.7290 (mpt180) cc_final: 0.6922 (mpt180) REVERT: K 103 MET cc_start: 0.6959 (mmt) cc_final: 0.5620 (mmt) REVERT: K 131 ASN cc_start: 0.8127 (OUTLIER) cc_final: 0.7848 (t0) REVERT: K 209 MET cc_start: 0.1949 (mmm) cc_final: 0.0116 (tmt) REVERT: K 286 ARG cc_start: 0.8483 (mmm160) cc_final: 0.8244 (mmm160) REVERT: K 368 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7034 (pp20) REVERT: G 1 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7231 (ppp) REVERT: G 34 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7018 (mtt180) REVERT: G 342 LEU cc_start: 0.1935 (OUTLIER) cc_final: 0.1582 (mp) REVERT: B 54 GLU cc_start: 0.6359 (OUTLIER) cc_final: 0.6112 (mp0) REVERT: B 63 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7267 (mp) REVERT: B 68 MET cc_start: 0.7445 (ttt) cc_final: 0.7179 (ttt) REVERT: B 78 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.6938 (mtt180) REVERT: B 155 LEU cc_start: 0.8088 (tp) cc_final: 0.7799 (tt) outliers start: 93 outliers final: 62 residues processed: 462 average time/residue: 0.5633 time to fit residues: 295.4295 Evaluate side-chains 492 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 416 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 82 GLN Chi-restraints excluded: chain F residue 163 SER 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 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 148 MET 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 224 GLU Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain I residue 320 SER 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 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 254 SER Chi-restraints excluded: chain K residue 271 VAL 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 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 34 ARG Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 172 GLN 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 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 193 VAL Chi-restraints excluded: chain B residue 206 GLN 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: 0.9980 chunk 31 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 210 optimal weight: 9.9990 chunk 71 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 225 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 J 17 ASN J 69 GLN J 349 ASN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 131 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.147020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.122863 restraints weight = 27808.572| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.16 r_work: 0.3505 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 19844 Z= 0.182 Angle : 0.609 8.999 27256 Z= 0.325 Chirality : 0.043 0.223 3067 Planarity : 0.004 0.112 3299 Dihedral : 16.789 151.175 3485 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.29 % Favored : 93.62 % Rotamer: Outliers : 4.92 % Allowed : 30.52 % 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: 0.00 (0.18), residues: 2288 helix: 1.22 (0.19), residues: 782 sheet: 0.65 (0.24), residues: 401 loop : -1.16 (0.19), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 286 TYR 0.043 0.001 TYR I 265 PHE 0.025 0.001 PHE J 189 TRP 0.081 0.002 TRP F 78 HIS 0.004 0.001 HIS K 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (19844) covalent geometry : angle 0.60929 / 0.32 (27256) hydrogen bonds : bond 0.03712 / 4.08 ( 806) hydrogen bonds : angle 4.32408 / 4.76 ( 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 513 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 422 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: F 52 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7127 (m-80) REVERT: F 63 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7964 (mtt-85) REVERT: F 78 TRP cc_start: 0.7961 (t60) cc_final: 0.7723 (t60) REVERT: F 209 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7855 (mtm) REVERT: F 310 ASP cc_start: 0.8097 (m-30) cc_final: 0.7870 (m-30) REVERT: F 323 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7806 (mp) REVERT: H 122 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7474 (tm) REVERT: H 365 LYS cc_start: 0.8181 (mppt) cc_final: 0.7768 (mppt) REVERT: H 370 GLN cc_start: 0.7473 (mt0) cc_final: 0.7231 (mt0) REVERT: I 111 LEU cc_start: 0.7841 (mm) cc_final: 0.7636 (mm) REVERT: J 102 PHE cc_start: 0.8522 (t80) cc_final: 0.8290 (t80) REVERT: J 135 GLN cc_start: 0.7960 (mt0) cc_final: 0.7707 (mt0) REVERT: J 168 GLU cc_start: 0.7558 (tp30) cc_final: 0.7336 (mp0) REVERT: J 251 THR cc_start: 0.8135 (OUTLIER) cc_final: 0.7891 (m) REVERT: K 18 ARG cc_start: 0.7445 (mpt180) cc_final: 0.7144 (mpt180) REVERT: K 131 ASN cc_start: 0.8250 (OUTLIER) cc_final: 0.7936 (t0) REVERT: K 209 MET cc_start: 0.1874 (mmm) cc_final: 0.0040 (tmt) REVERT: K 368 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7063 (pp20) REVERT: G 1 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7233 (ppp) REVERT: G 34 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7015 (mtt180) REVERT: G 209 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7932 (mtp) REVERT: G 342 LEU cc_start: 0.2106 (OUTLIER) cc_final: 0.1727 (mp) REVERT: B 54 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.6110 (mp0) REVERT: B 63 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7319 (mp) REVERT: B 68 MET cc_start: 0.7447 (ttt) cc_final: 0.7192 (ttt) outliers start: 91 outliers final: 63 residues processed: 467 average time/residue: 0.5335 time to fit residues: 282.9975 Evaluate side-chains 500 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 423 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 163 SER 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 224 GLU Chi-restraints excluded: chain H residue 256 LYS Chi-restraints excluded: chain H residue 361 ILE 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 148 MET 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 224 GLU Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain I residue 320 SER 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 K residue 56 LEU Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 298 GLU 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 34 ARG 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 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 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 190 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 147 optimal weight: 2.9990 chunk 162 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 221 optimal weight: 0.5980 chunk 208 optimal weight: 0.9980 chunk 172 optimal weight: 4.9990 chunk 218 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 200 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 127 GLN F 131 ASN H 17 ASN H 86 ASN H 164 ASN I 17 ASN I 127 GLN I 135 GLN I 152 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 131 ASN K 349 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.147540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.123425 restraints weight = 27669.907| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.15 r_work: 0.3513 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 19844 Z= 0.157 Angle : 0.601 9.880 27256 Z= 0.320 Chirality : 0.043 0.221 3067 Planarity : 0.004 0.112 3299 Dihedral : 16.765 151.986 3485 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.08 % Favored : 93.84 % 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: 0.04 (0.18), residues: 2288 helix: 1.23 (0.19), residues: 785 sheet: 0.65 (0.24), residues: 404 loop : -1.13 (0.19), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 286 TYR 0.047 0.001 TYR I 265 PHE 0.023 0.001 PHE J 189 TRP 0.088 0.002 TRP F 78 HIS 0.003 0.001 HIS K 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (19844) covalent geometry : angle 0.60091 / 0.32 (27256) hydrogen bonds : bond 0.03614 / 4.02 ( 806) hydrogen bonds : angle 4.27627 / 4.70 ( 2299) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8132.34 seconds wall clock time: 139 minutes 8.90 seconds (8348.90 seconds total)