Starting phenix.real_space_refine on Thu Sep 18 19:14:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zp9_60330/09_2025/8zp9_60330.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zp9_60330/09_2025/8zp9_60330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zp9_60330/09_2025/8zp9_60330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zp9_60330/09_2025/8zp9_60330.map" model { file = "/net/cci-nas-00/data/ceres_data/8zp9_60330/09_2025/8zp9_60330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zp9_60330/09_2025/8zp9_60330.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 429 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 73 5.49 5 S 74 5.16 5 C 11929 2.51 5 N 3392 2.21 5 O 3829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 4.60, per 1000 atoms: 0.24 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: 1.86 Conformation dependent library (CDL) restraints added in 865.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 2.11 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: 3.02 Time building geometry restraints manager: 2.34 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=" CB PRO B 179 " pdb=" CG PRO B 179 " ideal model delta sigma weight residual 1.492 1.606 -0.114 5.00e-02 4.00e+02 5.16e+00 bond pdb=" CG PRO K 334 " pdb=" CD PRO K 334 " ideal model delta sigma weight residual 1.503 1.577 -0.074 3.40e-02 8.65e+02 4.69e+00 bond pdb=" CB PRO J 151 " pdb=" CG PRO J 151 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.39e+00 bond pdb=" CB GLU B 144 " pdb=" CG GLU B 144 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.61e+00 bond pdb=" CB ASP J 117 " pdb=" CG ASP J 117 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.24e+00 ... (remaining 19839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 26924 2.39 - 4.79: 284 4.79 - 7.18: 37 7.18 - 9.58: 9 9.58 - 11.97: 2 Bond angle restraints: 27256 Sorted by residual: angle pdb=" CA GLU B 144 " pdb=" CB GLU B 144 " pdb=" CG GLU B 144 " ideal model delta sigma weight residual 114.10 122.14 -8.04 2.00e+00 2.50e-01 1.62e+01 angle pdb=" CA PRO B 179 " pdb=" N PRO B 179 " pdb=" CD PRO B 179 " ideal model delta sigma weight residual 112.00 106.74 5.26 1.40e+00 5.10e-01 1.41e+01 angle pdb=" N THR K 137 " pdb=" CA THR K 137 " pdb=" C THR K 137 " ideal model delta sigma weight residual 114.31 109.65 4.66 1.29e+00 6.01e-01 1.31e+01 angle pdb=" CA GLU K 74 " pdb=" CB GLU K 74 " pdb=" CG GLU K 74 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 angle pdb=" CA LEU I 120 " pdb=" CB LEU I 120 " pdb=" CG LEU I 120 " ideal model delta sigma weight residual 116.30 128.27 -11.97 3.50e+00 8.16e-02 1.17e+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: 2527 0.051 - 0.103: 449 0.103 - 0.154: 86 0.154 - 0.205: 3 0.205 - 0.257: 2 Chirality restraints: 3067 Sorted by residual: chirality pdb=" CG LEU B 44 " pdb=" CB LEU B 44 " pdb=" CD1 LEU B 44 " pdb=" CD2 LEU B 44 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA PRO J 151 " pdb=" N PRO J 151 " pdb=" C PRO J 151 " pdb=" CB PRO J 151 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB THR K 165 " pdb=" CA THR K 165 " pdb=" OG1 THR K 165 " pdb=" CG2 THR K 165 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.38e-01 ... (remaining 3064 not shown) Planarity restraints: 3299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU J 150 " -0.075 5.00e-02 4.00e+02 1.14e-01 2.07e+01 pdb=" N PRO J 151 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO J 151 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO J 151 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 238 " 0.045 5.00e-02 4.00e+02 6.87e-02 7.55e+00 pdb=" N PRO B 239 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 239 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 239 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 150 " 0.042 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO F 151 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO F 151 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 151 " 0.035 5.00e-02 4.00e+02 ... (remaining 3296 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 388 2.66 - 3.22: 17283 3.22 - 3.78: 30643 3.78 - 4.34: 41067 4.34 - 4.90: 67730 Nonbonded interactions: 157111 Sorted by model distance: nonbonded pdb=" OE2 GLU J 272 " pdb=" NZ LYS J 274 " model vdw 2.098 3.120 nonbonded pdb=" OE2 GLU I 4 " pdb=" OH TYR I 218 " model vdw 2.159 3.040 nonbonded pdb=" O2' C A 7 " pdb=" NH1 ARG F 18 " model vdw 2.161 3.120 nonbonded pdb=" OD1 ASP J 187 " pdb=" NH1 ARG K 36 " model vdw 2.165 3.120 nonbonded pdb=" O2' U A -6 " pdb=" OG SER B 38 " model vdw 2.173 3.040 ... (remaining 157106 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'F' and (resid 1 through 52 or (resid 53 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 69 or (resid 70 and (nam \ e N or name CA or name C or name O or name CB )) or resid 71 through 74 or (resi \ d 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throug \ h 78 or (resid 79 through 81 and (name N or name CA or name C or name O or name \ CB )) or resid 82 or (resid 83 and (name N or name CA or name C or name O or nam \ e CB )) or resid 84 through 86 or (resid 87 and (name N or name CA or name C or \ name O or name CB )) or resid 88 through 98 or (resid 99 and (name N or name CA \ or name C or name O or name CB )) or resid 100 through 104 or (resid 105 and (na \ me N or name CA or name C or name O or name CB )) or resid 106 through 117 or (r \ esid 118 and (name N or name CA or name C or name O or name CB )) or resid 119 o \ r (resid 120 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 21 or (resid 122 through 126 and (name N or name CA or name C or name O or name \ CB )) or resid 127 through 155 or (resid 156 and (name N or name CA or name C or \ name O or name CB )) or resid 157 through 159 or (resid 160 through 161 and (na \ me N or name CA or name C or name O or name CB )) or resid 162 through 184 or re \ sid 208 through 225 or (resid 226 and (name N or name CA or name C or name O or \ name CB )) or resid 227 or (resid 228 and (name N or name CA or name C or name O \ or name CB )) or resid 229 through 230 or (resid 231 and (name N or name CA or \ name C or name O or name CB )) or resid 232 through 256 or resid 263 through 291 \ or (resid 292 and (name N or name CA or name C or name O or name CB )) or resid \ 293 through 315 or (resid 316 through 319 and (name N or name CA or name C or n \ ame O or name CB )) or resid 320 through 338 or (resid 339 and (name N or name C \ A or name C or name O or name CB )) or resid 340 or (resid 341 and (name N or na \ me CA or name C or name O or name CB )) or resid 342 through 351 or (resid 352 a \ nd (name N or name CA or name C or name O or name CB )) or resid 353 through 368 \ or (resid 369 and (name N or name CA or name C or name O or name CB )) or resid \ 370 through 372)) selection = (chain 'H' and (resid 1 through 52 or (resid 53 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 69 or (resid 70 and (nam \ e N or name CA or name C or name O or name CB )) or resid 71 through 74 or (resi \ d 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throug \ h 79 or (resid 80 through 81 and (name N or name CA or name C or name O or name \ CB )) or resid 82 or (resid 83 and (name N or name CA or name C or name O or nam \ e CB )) or resid 84 through 90 or (resid 91 and (name N or name CA or name C or \ name O or name CB )) or resid 92 or resid 97 or (resid 98 through 99 and (name N \ or name CA or name C or name O or name CB )) or resid 100 through 104 or (resid \ 105 and (name N or name CA or name C or name O or name CB )) or resid 106 throu \ gh 117 or (resid 118 and (name N or name CA or name C or name O or name CB )) or \ resid 119 through 121 or (resid 122 through 126 and (name N or name CA or name \ C or name O or name CB )) or resid 127 through 152 or (resid 153 through 154 and \ (name N or name CA or name C or name O or name CB )) or resid 155 or (resid 156 \ and (name N or name CA or name C or name O or name CB )) or resid 157 through 1 \ 59 or (resid 160 through 161 and (name N or name CA or name C or name O or name \ CB )) or resid 162 through 184 or resid 208 through 225 or (resid 226 and (name \ N or name CA or name C or name O or name CB )) or resid 227 or (resid 228 and (n \ ame N or name CA or name C or name O or name CB )) or resid 229 through 230 or ( \ resid 231 and (name N or name CA or name C or name O or name CB )) or resid 232 \ through 256 or resid 263 through 291 or (resid 292 and (name N or name CA or nam \ e C or name O or name CB )) or resid 293 through 311 or (resid 312 and (name N o \ r name CA or name C or name O or name CB )) or resid 313 through 316 or (resid 3 \ 17 through 319 and (name N or name CA or name C or name O or name CB )) or resid \ 320 through 338 or (resid 339 and (name N or name CA or name C or name O or nam \ e CB )) or resid 340 or (resid 341 and (name N or name CA or name C or name O or \ name CB )) or resid 342 through 351 or (resid 352 and (name N or name CA or nam \ e C or name O or name CB )) or resid 353 through 364 or (resid 365 and (name N o \ r name CA or name C or name O or name CB )) or resid 366 through 367 or (resid 3 \ 68 through 369 and (name N or name CA or name C or name O or name CB )) or resid \ 370 through 372)) selection = (chain 'I' and (resid 1 through 52 or (resid 53 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 74 or (resid 75 and (nam \ e N or name CA or name C or name O or name CB )) or resid 76 through 78 or (resi \ d 79 through 81 and (name N or name CA or name C or name O or name CB )) or resi \ d 82 or (resid 83 and (name N or name CA or name C or name O or name CB )) or re \ sid 84 through 86 or (resid 87 and (name N or name CA or name C or name O or nam \ e CB )) or resid 88 through 90 or (resid 91 and (name N or name CA or name C or \ name O or name CB )) or resid 92 or resid 97 or (resid 98 through 99 and (name N \ or name CA or name C or name O or name CB )) or resid 100 through 104 or (resid \ 105 and (name N or name CA or name C or name O or name CB )) or resid 106 throu \ gh 108 or (resid 109 and (name N or name CA or name C or name O or name CB )) or \ resid 110 through 117 or (resid 118 and (name N or name CA or name C or name O \ or name CB )) or resid 119 or (resid 120 and (name N or name CA or name C or nam \ e O or name CB )) or resid 121 through 159 or (resid 160 through 161 and (name N \ or name CA or name C or name O or name CB )) or resid 162 through 184 or resid \ 208 through 225 or (resid 226 and (name N or name CA or name C or name O or name \ CB )) or resid 227 or (resid 228 and (name N or name CA or name C or name O or \ name CB )) or resid 229 through 256 or resid 263 through 311 or (resid 312 and ( \ name N or name CA or name C or name O or name CB )) or resid 313 through 315 or \ (resid 316 through 319 and (name N or name CA or name C or name O or name CB )) \ or resid 320 through 338 or (resid 339 and (name N or name CA or name C or name \ O or name CB )) or resid 340 through 351 or (resid 352 and (name N or name CA or \ name C or name O or name CB )) or resid 353 through 364 or (resid 365 and (name \ N or name CA or name C or name O or name CB )) or resid 366 through 367 or (res \ id 368 through 369 and (name N or name CA or name C or name O or name CB )) or r \ esid 370 or (resid 371 and (name N or name CA or name C or name O or name CB )) \ or resid 372)) selection = (chain 'J' and (resid 1 through 52 or (resid 53 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 69 or (resid 70 and (nam \ e N or name CA or name C or name O or name CB )) or resid 71 through 79 or (resi \ d 80 through 81 and (name N or name CA or name C or name O or name CB )) or resi \ d 82 through 86 or (resid 87 and (name N or name CA or name C or name O or name \ CB )) or resid 88 through 90 or (resid 91 and (name N or name CA or name C or na \ me O or name CB )) or resid 92 or resid 97 through 98 or (resid 99 and (name N o \ r name CA or name C or name O or name CB )) or resid 100 through 108 or (resid 1 \ 09 and (name N or name CA or name C or name O or name CB )) or resid 110 through \ 121 or (resid 122 through 126 and (name N or name CA or name C or name O or nam \ e CB )) or resid 127 through 152 or (resid 153 through 154 and (name N or name C \ A or name C or name O or name CB )) or resid 155 or (resid 156 and (name N or na \ me CA or name C or name O or name CB )) or resid 157 or (resid 158 through 161 a \ nd (name N or name CA or name C or name O or name CB )) or resid 162 through 184 \ or resid 208 through 225 or (resid 226 and (name N or name CA or name C or name \ O or name CB )) or resid 227 through 230 or (resid 231 and (name N or name CA o \ r name C or name O or name CB )) or resid 232 through 256 or resid 263 through 3 \ 11 or (resid 312 and (name N or name CA or name C or name O or name CB )) or res \ id 313 through 315 or (resid 316 through 319 and (name N or name CA or name C or \ name O or name CB )) or resid 320 through 351 or (resid 352 and (name N or name \ CA or name C or name O or name CB )) or resid 353 through 367 or (resid 368 thr \ ough 369 and (name N or name CA or name C or name O or name CB )) or resid 370 o \ r (resid 371 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 72)) selection = (chain 'K' and (resid 1 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 74 or (resid 75 and (name N or name \ CA or name C or name O or name CB )) or resid 76 through 78 or (resid 79 throug \ h 81 and (name N or name CA or name C or name O or name CB )) or resid 82 or (re \ sid 83 and (name N or name CA or name C or name O or name CB )) or resid 84 thro \ ugh 86 or (resid 87 and (name N or name CA or name C or name O or name CB )) or \ resid 88 through 90 or (resid 91 and (name N or name CA or name C or name O or n \ ame CB )) or resid 92 or resid 97 or (resid 98 through 99 and (name N or name CA \ or name C or name O or name CB )) or resid 100 through 104 or (resid 105 and (n \ ame N or name CA or name C or name O or name CB )) or resid 106 through 108 or ( \ resid 109 and (name N or name CA or name C or name O or name CB )) or resid 110 \ through 117 or (resid 118 and (name N or name CA or name C or name O or name CB \ )) or resid 119 or (resid 120 and (name N or name CA or name C or name O or name \ CB )) or resid 121 or (resid 122 through 126 and (name N or name CA or name C o \ r name O or name CB )) or resid 127 through 152 or (resid 153 through 154 and (n \ ame N or name CA or name C or name O or name CB )) or resid 155 or (resid 156 an \ d (name N or name CA or name C or name O or name CB )) or resid 157 through 159 \ or (resid 160 through 161 and (name N or name CA or name C or name O or name CB \ )) or resid 162 through 227 or (resid 228 and (name N or name CA or name C or na \ me O or name CB )) or resid 229 through 291 or (resid 292 and (name N or name CA \ or name C or name O or name CB )) or resid 293 through 311 or (resid 312 and (n \ ame N or name CA or name C or name O or name CB )) or resid 313 through 316 or ( \ resid 317 through 319 and (name N or name CA or name C or name O or name CB )) o \ r resid 320 through 338 or (resid 339 and (name N or name CA or name C or name O \ or name CB )) or resid 340 or (resid 341 and (name N or name CA or name C or na \ me O or name CB )) or resid 342 through 367 or (resid 368 through 369 and (name \ N or name CA or name C or name O or name CB )) or resid 370 through 372)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.040 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 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 : 0.003 0.114 19844 Z= 0.143 Angle : 0.630 11.975 27256 Z= 0.330 Chirality : 0.041 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 aren 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 covalent geometry : bond 0.00327 (19844) covalent geometry : angle 0.62973 (27256) hydrogen bonds : bond 0.18395 ( 806) hydrogen bonds : angle 6.50419 ( 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 : 0.735 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: 0.5505 time to fit residues: 295.0878 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: 0.2980 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: 0.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN H 164 ASN H 252 ASN H 370 GLN I 17 ASN I 82 GLN I 127 GLN I 306 ASN J 17 ASN J 204 HIS J 303 GLN J 349 ASN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 ASN K 131 ASN B 17 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.153649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.129207 restraints weight = 28096.722| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.18 r_work: 0.3594 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 19844 Z= 0.143 Angle : 0.592 11.109 27256 Z= 0.307 Chirality : 0.042 0.226 3067 Planarity : 0.005 0.114 3299 Dihedral : 16.701 133.519 3539 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.64 % Favored : 94.27 % Rotamer: Outliers : 5.47 % Allowed : 29.87 % 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 aren not related in a simple way. whole: 0.28 (0.18), residues: 2288 helix: 1.32 (0.20), residues: 786 sheet: 1.19 (0.24), residues: 411 loop : -1.10 (0.19), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 286 TYR 0.014 0.001 TYR I 265 PHE 0.014 0.001 PHE J 189 TRP 0.019 0.001 TRP B 59 HIS 0.002 0.001 HIS I 180 Details of bonding type rmsd covalent geometry : bond 0.00325 (19844) covalent geometry : angle 0.59220 (27256) hydrogen bonds : bond 0.03774 ( 806) hydrogen bonds : angle 4.44681 ( 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 547 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 446 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 63 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7798 (mtt-85) REVERT: F 103 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.6478 (pp-130) REVERT: F 127 GLN cc_start: 0.7832 (mm-40) cc_final: 0.7526 (tm-30) REVERT: F 148 MET cc_start: 0.7978 (pp-130) cc_final: 0.7654 (pp-130) REVERT: F 209 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7835 (mtm) REVERT: F 278 ILE cc_start: 0.8395 (mm) cc_final: 0.8123 (mt) REVERT: F 310 ASP cc_start: 0.7976 (m-30) cc_final: 0.7745 (m-30) REVERT: H 218 TYR cc_start: 0.8571 (t80) cc_final: 0.8111 (t80) REVERT: H 256 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8093 (mttt) REVERT: I 111 LEU cc_start: 0.7663 (mm) cc_final: 0.7407 (mm) REVERT: I 150 GLU cc_start: 0.7479 (mp0) cc_final: 0.7099 (tt0) REVERT: I 188 TYR cc_start: 0.8603 (t80) cc_final: 0.8341 (t80) REVERT: J 168 GLU cc_start: 0.7487 (tp30) cc_final: 0.7213 (mp0) REVERT: J 272 GLU cc_start: 0.7444 (pt0) cc_final: 0.7154 (pt0) REVERT: J 274 LYS cc_start: 0.7498 (ptpt) cc_final: 0.7165 (pttt) REVERT: J 330 ASN cc_start: 0.7928 (t0) cc_final: 0.7503 (t0) REVERT: K 18 ARG cc_start: 0.7237 (mpt180) cc_final: 0.6860 (mpt180) REVERT: K 131 ASN cc_start: 0.8059 (OUTLIER) cc_final: 0.7682 (t0) REVERT: K 209 MET cc_start: 0.2555 (mmm) cc_final: 0.0924 (tmt) REVERT: B 68 MET cc_start: 0.7319 (ttt) cc_final: 0.6956 (ttt) REVERT: B 78 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.7027 (mmt180) REVERT: B 129 ARG cc_start: 0.8194 (mmt90) cc_final: 0.7992 (mmt180) outliers start: 101 outliers final: 36 residues processed: 496 average time/residue: 0.5674 time to fit residues: 317.5969 Evaluate side-chains 455 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 413 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 74 GLU Chi-restraints excluded: chain H residue 114 ILE 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 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 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 361 ILE Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain K residue 246 LEU Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 172 GLN Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain 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 78 ARG 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: 6.9990 chunk 201 optimal weight: 0.0670 chunk 53 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 ASN ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN H 131 ASN H 164 ASN I 17 ASN I 127 GLN I 306 ASN J 17 ASN J 69 GLN J 86 ASN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 ASN ** K 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 = 0.3927 r_free = 0.3927 target = 0.146646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.122685 restraints weight = 27861.098| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.32 r_work: 0.3492 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 19844 Z= 0.231 Angle : 0.658 10.096 27256 Z= 0.343 Chirality : 0.045 0.268 3067 Planarity : 0.005 0.115 3299 Dihedral : 16.826 126.540 3491 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.03 % Favored : 93.88 % Rotamer: Outliers : 6.82 % Allowed : 27.92 % Favored : 65.26 % 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 aren not related in a simple way. whole: 0.01 (0.18), residues: 2288 helix: 1.06 (0.19), residues: 782 sheet: 0.92 (0.24), residues: 412 loop : -1.16 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 286 TYR 0.018 0.002 TYR I 265 PHE 0.025 0.002 PHE J 189 TRP 0.032 0.002 TRP B 59 HIS 0.005 0.001 HIS J 239 Details of bonding type rmsd covalent geometry : bond 0.00526 (19844) covalent geometry : angle 0.65763 (27256) hydrogen bonds : bond 0.04329 ( 806) hydrogen bonds : angle 4.53666 ( 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 573 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 447 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 52 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7381 (m-80) REVERT: F 63 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.8023 (mtt-85) REVERT: F 103 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.6577 (pp-130) REVERT: F 127 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7780 (tm-30) REVERT: F 209 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.7874 (mtm) REVERT: F 278 ILE cc_start: 0.8402 (mm) cc_final: 0.8185 (mt) REVERT: H 74 GLU cc_start: 0.7640 (mp0) cc_final: 0.7327 (mp0) REVERT: H 122 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7480 (tm) REVERT: H 256 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8009 (mttt) REVERT: H 370 GLN cc_start: 0.7412 (mt0) cc_final: 0.7171 (mt0) REVERT: I 111 LEU cc_start: 0.7866 (mm) cc_final: 0.7665 (mm) REVERT: J 135 GLN cc_start: 0.7982 (mt0) cc_final: 0.7745 (mt0) REVERT: J 168 GLU cc_start: 0.7620 (tp30) cc_final: 0.7342 (mp0) REVERT: K 18 ARG cc_start: 0.7438 (mpt180) cc_final: 0.6862 (mpt180) REVERT: K 44 ARG cc_start: 0.8534 (ttt90) cc_final: 0.8281 (ttt-90) REVERT: K 46 ILE cc_start: 0.8354 (mt) cc_final: 0.8149 (mt) REVERT: K 103 MET cc_start: 0.7243 (mmt) cc_final: 0.6093 (mmt) REVERT: K 131 ASN cc_start: 0.8044 (t0) cc_final: 0.7794 (t0) REVERT: K 246 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8053 (mp) REVERT: K 303 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.8004 (mt0) REVERT: K 368 GLU cc_start: 0.7519 (pp20) cc_final: 0.7032 (pp20) REVERT: G 1 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7288 (ppp) REVERT: G 224 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8052 (mm-30) REVERT: G 342 LEU cc_start: 0.1907 (OUTLIER) cc_final: 0.1568 (mp) REVERT: G 360 TYR cc_start: 0.8557 (t80) cc_final: 0.8335 (t80) REVERT: B 63 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7592 (mt) outliers start: 126 outliers final: 57 residues processed: 509 average time/residue: 0.5359 time to fit residues: 308.4920 Evaluate side-chains 490 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 422 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 275 ASN Chi-restraints excluded: chain F residue 292 LYS Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 133 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 224 GLU Chi-restraints excluded: chain H residue 256 LYS Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 91 LYS Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 293 GLU 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 181 ILE Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain K residue 246 LEU Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 303 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 46 ILE 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 221 ILE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 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 185 THR Chi-restraints excluded: chain B residue 247 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 101 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 202 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 180 HIS H 17 ASN H 86 ASN H 164 ASN H 225 GLN I 17 ASN I 127 GLN I 306 ASN J 17 ASN J 69 GLN J 127 GLN J 349 ASN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 ASN ** K 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 349 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.147330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.123491 restraints weight = 27723.630| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.15 r_work: 0.3512 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2214 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= 0.172 Angle : 0.599 10.056 27256 Z= 0.310 Chirality : 0.042 0.227 3067 Planarity : 0.004 0.114 3299 Dihedral : 16.579 117.511 3487 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.59 % Favored : 94.32 % Rotamer: Outliers : 5.30 % Allowed : 29.22 % Favored : 65.48 % 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 aren not related in a simple way. whole: 0.06 (0.18), residues: 2288 helix: 1.16 (0.19), residues: 788 sheet: 0.83 (0.24), residues: 415 loop : -1.14 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 286 TYR 0.019 0.001 TYR I 265 PHE 0.017 0.001 PHE J 189 TRP 0.031 0.001 TRP B 59 HIS 0.003 0.001 HIS I 180 Details of bonding type rmsd covalent geometry : bond 0.00391 (19844) covalent geometry : angle 0.59858 (27256) hydrogen bonds : bond 0.03637 ( 806) hydrogen bonds : angle 4.28895 ( 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 535 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 437 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 52 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7358 (m-80) REVERT: F 63 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7855 (mtt-85) REVERT: F 107 LYS cc_start: 0.7446 (tppp) cc_final: 0.7076 (tppp) REVERT: F 209 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.7829 (mtm) REVERT: F 323 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7940 (mp) REVERT: H 74 GLU cc_start: 0.7540 (mp0) cc_final: 0.7220 (mp0) REVERT: H 122 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7380 (tm) REVERT: H 127 GLN cc_start: 0.7826 (tp40) cc_final: 0.7596 (tp40) REVERT: H 218 TYR cc_start: 0.8610 (t80) cc_final: 0.8300 (t80) REVERT: H 370 GLN cc_start: 0.7436 (mt0) cc_final: 0.7149 (mt0) REVERT: I 368 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7430 (pm20) REVERT: J 1 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.6681 (ppp) REVERT: J 135 GLN cc_start: 0.7888 (mt0) cc_final: 0.7674 (mt0) REVERT: J 168 GLU cc_start: 0.7564 (tp30) cc_final: 0.7327 (mp0) REVERT: J 251 THR cc_start: 0.8088 (OUTLIER) cc_final: 0.7849 (m) REVERT: K 18 ARG cc_start: 0.7444 (mpt180) cc_final: 0.7070 (mpt180) REVERT: K 32 VAL cc_start: 0.8168 (m) cc_final: 0.7741 (p) REVERT: K 46 ILE cc_start: 0.8346 (mt) cc_final: 0.8138 (mt) REVERT: K 103 MET cc_start: 0.6937 (mmt) cc_final: 0.5688 (mmt) REVERT: K 131 ASN cc_start: 0.8166 (t0) cc_final: 0.7812 (t0) REVERT: K 209 MET cc_start: 0.2054 (mmm) cc_final: 0.0257 (tmt) REVERT: K 368 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7029 (pp20) REVERT: G 1 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7239 (ppp) REVERT: G 360 TYR cc_start: 0.8540 (t80) cc_final: 0.8330 (t80) REVERT: B 68 MET cc_start: 0.7282 (ttt) cc_final: 0.6860 (ttt) REVERT: B 155 LEU cc_start: 0.8168 (tp) cc_final: 0.7922 (tt) outliers start: 98 outliers final: 50 residues processed: 486 average time/residue: 0.5852 time to fit residues: 321.4849 Evaluate side-chains 484 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 424 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 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 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 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 59 VAL 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 224 GLU Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain I residue 368 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain J residue 53 LYS 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 132 VAL Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 347 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 148 MET Chi-restraints excluded: chain G residue 172 GLN 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 347 ILE Chi-restraints excluded: chain B residue 38 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 125 optimal weight: 0.7980 chunk 232 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 166 optimal weight: 0.1980 chunk 160 optimal weight: 0.9980 chunk 184 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN H 86 ASN H 164 ASN I 17 ASN I 127 GLN J 17 ASN J 69 GLN J 86 ASN J 127 GLN J 225 GLN J 349 ASN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 ASN ** K 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 235 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 = 0.3932 r_free = 0.3932 target = 0.146952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.123384 restraints weight = 27709.117| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.33 r_work: 0.3497 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2362 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= 0.159 Angle : 0.592 9.789 27256 Z= 0.306 Chirality : 0.042 0.224 3067 Planarity : 0.004 0.112 3299 Dihedral : 16.457 112.122 3485 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.12 % Favored : 93.79 % Rotamer: Outliers : 5.79 % Allowed : 28.68 % Favored : 65.53 % 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 aren not related in a simple way. whole: 0.10 (0.18), residues: 2288 helix: 1.21 (0.19), residues: 789 sheet: 0.77 (0.24), residues: 415 loop : -1.10 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 286 TYR 0.020 0.001 TYR I 265 PHE 0.017 0.001 PHE J 189 TRP 0.033 0.001 TRP B 59 HIS 0.003 0.001 HIS I 180 Details of bonding type rmsd covalent geometry : bond 0.00364 (19844) covalent geometry : angle 0.59208 (27256) hydrogen bonds : bond 0.03573 ( 806) hydrogen bonds : angle 4.24326 ( 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 544 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 437 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 52 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7254 (m-80) REVERT: F 63 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7839 (mtt-85) REVERT: F 147 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7720 (ptt90) REVERT: F 209 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7900 (mtm) REVERT: F 323 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.7925 (mp) REVERT: H 122 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7439 (tm) REVERT: H 127 GLN cc_start: 0.7887 (tp40) cc_final: 0.7673 (tp40) REVERT: H 218 TYR cc_start: 0.8590 (t80) cc_final: 0.8282 (t80) REVERT: H 256 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8034 (mttt) REVERT: H 368 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6672 (pp20) REVERT: I 368 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7410 (pm20) REVERT: J 103 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7509 (ptp) REVERT: J 168 GLU cc_start: 0.7563 (tp30) cc_final: 0.7319 (mp0) REVERT: J 251 THR cc_start: 0.8143 (OUTLIER) cc_final: 0.7890 (m) REVERT: J 278 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7752 (mt) REVERT: K 18 ARG cc_start: 0.7384 (mpt180) cc_final: 0.6768 (mpt180) REVERT: K 103 MET cc_start: 0.6899 (mmt) cc_final: 0.5694 (mmt) REVERT: K 131 ASN cc_start: 0.8166 (t0) cc_final: 0.7695 (t0) REVERT: K 368 GLU cc_start: 0.7531 (pp20) cc_final: 0.7074 (pp20) REVERT: G 1 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7234 (ppp) REVERT: G 342 LEU cc_start: 0.2352 (OUTLIER) cc_final: 0.1770 (mp) REVERT: G 345 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7718 (mtm110) REVERT: G 360 TYR cc_start: 0.8551 (t80) cc_final: 0.8340 (t80) REVERT: B 54 GLU cc_start: 0.6378 (OUTLIER) cc_final: 0.6086 (mp0) REVERT: B 68 MET cc_start: 0.7358 (ttt) cc_final: 0.7029 (ttt) outliers start: 107 outliers final: 54 residues processed: 497 average time/residue: 0.6086 time to fit residues: 340.6141 Evaluate side-chains 486 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 416 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 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 133 ILE 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 181 ILE Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 256 LYS Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain I residue 91 LYS Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 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 368 GLU Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 103 MET Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 145 CYS Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 246 LEU Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 361 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 26 THR 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 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 127 SER Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 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: 0.8980 chunk 83 optimal weight: 0.1980 chunk 200 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 17 ASN F 82 GLN ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN H 86 ASN H 164 ASN H 370 GLN I 17 ASN I 127 GLN I 349 ASN J 17 ASN J 69 GLN J 127 GLN J 152 ASN J 330 ASN J 349 ASN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN K 118 ASN ** K 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 303 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.143656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.120213 restraints weight = 27434.046| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.35 r_work: 0.3453 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2803 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= 0.224 Angle : 0.650 10.523 27256 Z= 0.337 Chirality : 0.045 0.240 3067 Planarity : 0.005 0.111 3299 Dihedral : 16.594 107.733 3485 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.21 % Favored : 93.71 % 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 aren not related in a simple way. whole: -0.06 (0.18), residues: 2288 helix: 1.05 (0.19), residues: 787 sheet: 0.65 (0.24), residues: 420 loop : -1.16 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 18 TYR 0.023 0.001 TYR I 265 PHE 0.021 0.002 PHE J 189 TRP 0.036 0.002 TRP B 59 HIS 0.005 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00514 (19844) covalent geometry : angle 0.65008 (27256) hydrogen bonds : bond 0.03995 ( 806) hydrogen bonds : angle 4.41815 ( 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 575 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 462 time to evaluate : 0.764 Fit side-chains REVERT: F 52 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7834 (m-80) REVERT: F 63 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7976 (mtt-85) REVERT: F 127 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7690 (tm-30) REVERT: F 209 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.7892 (mtm) REVERT: F 254 SER cc_start: 0.8292 (t) cc_final: 0.7897 (p) REVERT: F 323 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8013 (mp) REVERT: H 122 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7398 (tm) REVERT: H 138 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8297 (tt) REVERT: H 256 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7991 (mttt) REVERT: H 368 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6639 (pp20) REVERT: H 370 GLN cc_start: 0.7801 (mt0) cc_final: 0.7599 (mt0) REVERT: I 368 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7401 (pm20) REVERT: J 63 ARG cc_start: 0.8437 (ptp-170) cc_final: 0.8195 (ptp-170) REVERT: J 135 GLN cc_start: 0.7859 (mt0) cc_final: 0.7630 (mt0) REVERT: J 278 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7861 (mt) REVERT: K 131 ASN cc_start: 0.8215 (t0) cc_final: 0.7760 (t0) REVERT: K 138 LEU cc_start: 0.8456 (mm) cc_final: 0.8219 (mp) REVERT: G 1 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7304 (ppp) REVERT: B 54 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.6139 (mp0) REVERT: B 68 MET cc_start: 0.7392 (ttt) cc_final: 0.7107 (ttt) outliers start: 113 outliers final: 62 residues processed: 518 average time/residue: 0.5769 time to fit residues: 338.7466 Evaluate side-chains 512 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 438 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 55 LEU 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 114 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 148 MET Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 256 LYS Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain I residue 91 LYS Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 165 THR 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 195 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 368 GLU Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain J residue 53 LYS 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 122 LEU Chi-restraints excluded: chain J residue 132 VAL 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 278 ILE Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 298 GLU 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 3 ILE Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 144 LEU 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 221 ILE 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 347 ILE Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 247 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 82 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 133 optimal weight: 0.0980 chunk 93 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 202 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 139 optimal weight: 0.1980 chunk 148 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN H 86 ASN H 164 ASN I 17 ASN I 127 GLN J 17 ASN J 69 GLN J 86 ASN J 349 ASN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 ASN ** K 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 349 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.146154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.122670 restraints weight = 27627.144| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.32 r_work: 0.3493 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 19844 Z= 0.137 Angle : 0.601 9.827 27256 Z= 0.309 Chirality : 0.042 0.245 3067 Planarity : 0.004 0.109 3299 Dihedral : 16.318 106.249 3484 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.81 % Favored : 94.10 % Rotamer: Outliers : 4.76 % Allowed : 30.68 % 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 aren not related in a simple way. whole: 0.06 (0.18), residues: 2288 helix: 1.14 (0.19), residues: 796 sheet: 0.70 (0.24), residues: 419 loop : -1.07 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 286 TYR 0.018 0.001 TYR I 265 PHE 0.016 0.001 PHE J 189 TRP 0.049 0.001 TRP F 78 HIS 0.004 0.001 HIS I 180 Details of bonding type rmsd covalent geometry : bond 0.00312 (19844) covalent geometry : angle 0.60084 (27256) hydrogen bonds : bond 0.03456 ( 806) hydrogen bonds : angle 4.18568 ( 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 520 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 432 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 52 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7607 (m-80) REVERT: F 63 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7783 (ptp-170) REVERT: F 127 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7572 (tm-30) REVERT: F 250 LYS cc_start: 0.8540 (mtmm) cc_final: 0.8205 (mtmm) REVERT: F 323 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7942 (mp) REVERT: H 122 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7362 (tm) REVERT: H 218 TYR cc_start: 0.8610 (t80) cc_final: 0.8318 (t80) REVERT: H 251 THR cc_start: 0.8561 (p) cc_final: 0.8298 (t) REVERT: H 256 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8093 (mttt) REVERT: H 368 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6644 (pp20) REVERT: I 111 LEU cc_start: 0.7571 (mm) cc_final: 0.7307 (mm) REVERT: I 365 LYS cc_start: 0.8213 (mmtm) cc_final: 0.7646 (mmmm) REVERT: I 368 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7334 (pm20) REVERT: J 135 GLN cc_start: 0.7825 (mt0) cc_final: 0.7575 (mt0) REVERT: J 168 GLU cc_start: 0.7571 (tp30) cc_final: 0.7306 (mp0) REVERT: J 278 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7716 (mt) REVERT: K 18 ARG cc_start: 0.7321 (mpt180) cc_final: 0.6744 (mpt180) REVERT: K 103 MET cc_start: 0.6937 (mmt) cc_final: 0.5958 (mmt) REVERT: K 131 ASN cc_start: 0.8118 (t0) cc_final: 0.7678 (t0) REVERT: K 138 LEU cc_start: 0.8377 (mm) cc_final: 0.8144 (mp) REVERT: K 209 MET cc_start: 0.1600 (mmm) cc_final: -0.0188 (tmt) REVERT: G 1 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7309 (ppp) REVERT: G 193 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7750 (t0) REVERT: B 54 GLU cc_start: 0.6371 (OUTLIER) cc_final: 0.6113 (mp0) outliers start: 88 outliers final: 47 residues processed: 479 average time/residue: 0.6013 time to fit residues: 325.8121 Evaluate side-chains 478 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 420 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 79 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 114 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 256 LYS Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 165 THR 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 368 GLU Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain J residue 53 LYS 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 122 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 278 ILE Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 298 GLU Chi-restraints excluded: chain K residue 347 ILE 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 144 LEU Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 193 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 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 185 THR 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: 0.2980 chunk 67 optimal weight: 2.9990 chunk 234 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 224 optimal weight: 0.2980 chunk 203 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 170 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 ASN ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 HIS ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN H 127 GLN H 164 ASN H 257 GLN H 299 GLN H 370 GLN I 17 ASN I 127 GLN J 17 ASN J 69 GLN J 349 ASN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.145622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.122029 restraints weight = 27681.283| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.27 r_work: 0.3486 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2876 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= 0.145 Angle : 0.602 10.064 27256 Z= 0.309 Chirality : 0.042 0.223 3067 Planarity : 0.004 0.108 3299 Dihedral : 16.176 104.839 3479 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.03 % Favored : 93.88 % Rotamer: Outliers : 4.49 % Allowed : 30.68 % Favored : 64.83 % 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 aren not related in a simple way. whole: 0.13 (0.18), residues: 2288 helix: 1.26 (0.19), residues: 788 sheet: 0.69 (0.24), residues: 421 loop : -1.07 (0.19), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 18 TYR 0.021 0.001 TYR I 265 PHE 0.026 0.001 PHE K 273 TRP 0.059 0.002 TRP F 78 HIS 0.003 0.001 HIS J 204 Details of bonding type rmsd covalent geometry : bond 0.00331 (19844) covalent geometry : angle 0.60212 (27256) hydrogen bonds : bond 0.03427 ( 806) hydrogen bonds : angle 4.13448 ( 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 512 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 429 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 52 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7437 (m-80) REVERT: F 63 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7556 (mtt-85) REVERT: F 78 TRP cc_start: 0.7913 (t60) cc_final: 0.7660 (t60) REVERT: F 82 GLN cc_start: 0.7879 (mt0) cc_final: 0.7666 (mt0) REVERT: F 127 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7540 (tm-30) REVERT: F 250 LYS cc_start: 0.8548 (mtmm) cc_final: 0.8264 (mtmm) REVERT: F 310 ASP cc_start: 0.8083 (m-30) cc_final: 0.7859 (m-30) REVERT: F 323 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7910 (mp) REVERT: H 122 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7362 (tm) REVERT: H 127 GLN cc_start: 0.7791 (tp40) cc_final: 0.7590 (tp40) REVERT: H 218 TYR cc_start: 0.8599 (t80) cc_final: 0.8342 (t80) REVERT: H 251 THR cc_start: 0.8529 (p) cc_final: 0.8278 (t) REVERT: H 256 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8094 (mttt) REVERT: H 368 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6601 (pp20) REVERT: I 111 LEU cc_start: 0.7609 (mm) cc_final: 0.7379 (mm) REVERT: I 365 LYS cc_start: 0.8216 (mmtm) cc_final: 0.7651 (mmmm) REVERT: I 368 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7343 (pm20) REVERT: J 168 GLU cc_start: 0.7601 (tp30) cc_final: 0.7340 (mp0) REVERT: J 272 GLU cc_start: 0.7378 (pt0) cc_final: 0.7166 (pt0) REVERT: K 18 ARG cc_start: 0.7300 (mpt180) cc_final: 0.6835 (mpt180) REVERT: K 103 MET cc_start: 0.7032 (mmt) cc_final: 0.5990 (mmt) REVERT: K 131 ASN cc_start: 0.8129 (t0) cc_final: 0.7704 (t0) REVERT: K 148 MET cc_start: 0.8199 (tmt) cc_final: 0.7836 (ttt) REVERT: K 168 GLU cc_start: 0.7407 (pm20) cc_final: 0.7183 (pm20) REVERT: K 240 THR cc_start: 0.8441 (m) cc_final: 0.8227 (m) REVERT: K 246 LEU cc_start: 0.8321 (mt) cc_final: 0.7991 (mp) REVERT: K 368 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7082 (pp20) REVERT: G 1 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7276 (ppp) REVERT: G 193 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7718 (t0) REVERT: G 222 ASP cc_start: 0.6495 (OUTLIER) cc_final: 0.6219 (p0) REVERT: G 345 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7741 (mtm110) REVERT: B 54 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.6104 (mp0) REVERT: B 68 MET cc_start: 0.7109 (ttt) cc_final: 0.6686 (ttt) outliers start: 83 outliers final: 52 residues processed: 472 average time/residue: 0.6014 time to fit residues: 320.1740 Evaluate side-chains 498 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 433 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 79 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 183 ARG 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 H residue 368 GLU Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 195 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 368 GLU 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 122 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 K residue 56 LEU Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 298 GLU Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 361 ILE Chi-restraints excluded: chain K residue 368 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 212 SER Chi-restraints excluded: chain G residue 222 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 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 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: 3.9990 chunk 180 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 232 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 217 optimal weight: 0.0010 chunk 48 optimal weight: 1.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 ASN ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN H 164 ASN H 370 GLN I 17 ASN I 127 GLN J 17 ASN J 69 GLN J 86 ASN J 330 ASN J 349 ASN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.142804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.119147 restraints weight = 27383.114| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.26 r_work: 0.3446 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3132 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= 0.215 Angle : 0.663 9.325 27256 Z= 0.343 Chirality : 0.045 0.236 3067 Planarity : 0.005 0.107 3299 Dihedral : 16.356 103.773 3479 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.34 % Favored : 93.58 % Rotamer: Outliers : 4.33 % Allowed : 31.28 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.18), residues: 2288 helix: 1.14 (0.19), residues: 779 sheet: 0.57 (0.24), residues: 419 loop : -1.16 (0.19), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 113 TYR 0.018 0.002 TYR F 360 PHE 0.030 0.002 PHE J 189 TRP 0.061 0.002 TRP F 78 HIS 0.005 0.001 HIS J 6 Details of bonding type rmsd covalent geometry : bond 0.00494 (19844) covalent geometry : angle 0.66273 (27256) hydrogen bonds : bond 0.03844 ( 806) hydrogen bonds : angle 4.36006 ( 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 514 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 434 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: F 52 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7835 (m-80) REVERT: F 63 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7619 (ptp-170) REVERT: F 127 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7753 (tm-30) REVERT: F 209 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7872 (mtm) REVERT: F 250 LYS cc_start: 0.8586 (mtmm) cc_final: 0.8281 (mtmm) REVERT: F 323 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.7947 (mp) REVERT: H 122 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7447 (tm) REVERT: H 218 TYR cc_start: 0.8591 (t80) cc_final: 0.8367 (t80) REVERT: H 256 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8047 (mttt) REVERT: H 368 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6590 (pp20) REVERT: I 368 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7395 (pm20) REVERT: J 135 GLN cc_start: 0.7871 (mt0) cc_final: 0.7611 (mt0) REVERT: J 272 GLU cc_start: 0.7393 (pt0) cc_final: 0.7077 (pt0) REVERT: K 18 ARG cc_start: 0.7425 (mpt180) cc_final: 0.7041 (mpt180) REVERT: K 131 ASN cc_start: 0.8177 (t0) cc_final: 0.7783 (t0) REVERT: K 246 LEU cc_start: 0.8363 (mt) cc_final: 0.7960 (mp) REVERT: K 368 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7112 (pp20) REVERT: G 1 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7276 (ppp) REVERT: G 193 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7695 (t70) REVERT: G 222 ASP cc_start: 0.6504 (OUTLIER) cc_final: 0.6207 (p0) REVERT: G 345 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7744 (mtm110) outliers start: 80 outliers final: 56 residues processed: 477 average time/residue: 0.5938 time to fit residues: 319.5036 Evaluate side-chains 488 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 419 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 152 ASN 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 114 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 148 MET Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 183 ARG Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 256 LYS Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 195 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 368 GLU Chi-restraints excluded: chain J residue 53 LYS 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 122 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 260 PHE Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 298 GLU Chi-restraints excluded: chain K residue 309 ASN Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 361 ILE Chi-restraints excluded: chain K residue 368 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 212 SER Chi-restraints excluded: chain G residue 222 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 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 164 LEU 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: 0.7980 chunk 31 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 210 optimal weight: 10.0000 chunk 71 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 225 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 134 optimal weight: 0.0470 chunk 14 optimal weight: 1.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 ASN F 82 GLN ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN H 86 ASN H 164 ASN H 204 HIS H 370 GLN I 17 ASN I 127 GLN J 17 ASN J 69 GLN J 70 GLN J 349 ASN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.144626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.121201 restraints weight = 27736.687| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.29 r_work: 0.3475 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 19844 Z= 0.143 Angle : 0.621 9.664 27256 Z= 0.318 Chirality : 0.042 0.228 3067 Planarity : 0.004 0.105 3299 Dihedral : 16.219 105.167 3479 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.86 % Favored : 94.06 % Rotamer: Outliers : 4.33 % Allowed : 31.60 % Favored : 64.07 % 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 aren not related in a simple way. whole: 0.04 (0.18), residues: 2288 helix: 1.21 (0.19), residues: 787 sheet: 0.58 (0.24), residues: 422 loop : -1.10 (0.19), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 18 TYR 0.018 0.001 TYR F 360 PHE 0.026 0.001 PHE K 102 TRP 0.064 0.002 TRP F 78 HIS 0.003 0.001 HIS J 239 Details of bonding type rmsd covalent geometry : bond 0.00329 (19844) covalent geometry : angle 0.62091 (27256) hydrogen bonds : bond 0.03403 ( 806) hydrogen bonds : angle 4.20281 ( 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 491 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 411 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: F 52 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7679 (m-80) REVERT: F 63 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7792 (ptp-170) REVERT: F 127 GLN cc_start: 0.7933 (mm-40) cc_final: 0.7555 (tm-30) REVERT: F 250 LYS cc_start: 0.8557 (mtmm) cc_final: 0.8274 (mtmm) REVERT: F 310 ASP cc_start: 0.8094 (m-30) cc_final: 0.7877 (m-30) REVERT: F 323 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7924 (mp) REVERT: H 74 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: H 122 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7384 (tm) REVERT: H 218 TYR cc_start: 0.8619 (t80) cc_final: 0.8383 (t80) REVERT: H 256 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8077 (mttt) REVERT: H 368 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6542 (pp20) REVERT: I 111 LEU cc_start: 0.7605 (mm) cc_final: 0.7385 (mm) REVERT: I 368 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7392 (pm20) REVERT: J 103 MET cc_start: 0.7913 (ppp) cc_final: 0.7481 (ptp) REVERT: J 168 GLU cc_start: 0.7581 (tp30) cc_final: 0.7314 (mp0) REVERT: J 272 GLU cc_start: 0.7394 (pt0) cc_final: 0.7103 (pt0) REVERT: K 18 ARG cc_start: 0.7366 (mpt180) cc_final: 0.7013 (mpt180) REVERT: K 103 MET cc_start: 0.7118 (mmt) cc_final: 0.6145 (mmt) REVERT: K 131 ASN cc_start: 0.8127 (t0) cc_final: 0.7698 (t0) REVERT: K 240 THR cc_start: 0.8448 (m) cc_final: 0.8247 (m) REVERT: K 246 LEU cc_start: 0.8338 (mt) cc_final: 0.7925 (mp) REVERT: K 368 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7138 (pp20) REVERT: G 1 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7233 (ppp) REVERT: G 193 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7772 (t0) REVERT: G 222 ASP cc_start: 0.6448 (OUTLIER) cc_final: 0.6169 (p0) REVERT: G 345 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7737 (mtm110) REVERT: B 68 MET cc_start: 0.7109 (ttt) cc_final: 0.6747 (ttt) outliers start: 80 outliers final: 54 residues processed: 454 average time/residue: 0.6422 time to fit residues: 328.3072 Evaluate side-chains 482 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 415 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 163 SER 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 183 ARG Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 256 LYS Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 195 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 368 GLU Chi-restraints excluded: chain J residue 53 LYS 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 122 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 260 PHE Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 181 ILE Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 298 GLU Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 361 ILE Chi-restraints excluded: chain K residue 368 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 212 SER Chi-restraints excluded: chain G residue 222 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 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 164 LEU 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: 4.9990 chunk 162 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 chunk 208 optimal weight: 0.0770 chunk 172 optimal weight: 4.9990 chunk 218 optimal weight: 6.9990 chunk 170 optimal weight: 0.9980 chunk 13 optimal weight: 0.0770 chunk 200 optimal weight: 0.0980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 ASN F 82 GLN ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN H 86 ASN H 164 ASN I 17 ASN I 127 GLN J 17 ASN J 69 GLN J 70 GLN J 349 ASN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.145965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.122625 restraints weight = 27743.776| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.29 r_work: 0.3497 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 19844 Z= 0.128 Angle : 0.600 9.761 27256 Z= 0.307 Chirality : 0.042 0.220 3067 Planarity : 0.004 0.104 3299 Dihedral : 16.069 102.033 3479 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.25 % Favored : 93.66 % Rotamer: Outliers : 3.90 % Allowed : 32.03 % Favored : 64.07 % 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 aren not related in a simple way. whole: 0.13 (0.18), residues: 2288 helix: 1.26 (0.19), residues: 789 sheet: 0.72 (0.24), residues: 417 loop : -1.07 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 18 TYR 0.016 0.001 TYR F 360 PHE 0.025 0.001 PHE K 273 TRP 0.068 0.002 TRP F 78 HIS 0.003 0.001 HIS I 339 Details of bonding type rmsd covalent geometry : bond 0.00294 (19844) covalent geometry : angle 0.60046 (27256) hydrogen bonds : bond 0.03186 ( 806) hydrogen bonds : angle 4.08419 ( 2299) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8388.66 seconds wall clock time: 143 minutes 22.01 seconds (8602.01 seconds total)