Starting phenix.real_space_refine on Tue Jun 17 03:38:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zp9_60330/06_2025/8zp9_60330.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zp9_60330/06_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_60330/06_2025/8zp9_60330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zp9_60330/06_2025/8zp9_60330.map" model { file = "/net/cci-nas-00/data/ceres_data/8zp9_60330/06_2025/8zp9_60330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zp9_60330/06_2025/8zp9_60330.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP: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, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP: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, 'ASN:plan1': 1, 'HIS:plan': 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: {'GLU:plan': 1, 'ARG: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: 12.81, per 1000 atoms: 0.66 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: 5.32 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 6.76 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: 6.88 Time building geometry restraints manager: 6.26 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: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 51.730 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.770 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.037 0.001 TRP B 59 HIS 0.003 0.001 HIS J 6 PHE 0.021 0.001 PHE B 82 TYR 0.025 0.001 TYR J 360 ARG 0.010 0.001 ARG I 286 Details of bonding type rmsd hydrogen bonds : bond 0.18395 ( 806) hydrogen bonds : angle 6.50419 ( 2299) covalent geometry : bond 0.00327 (19844) covalent geometry : angle 0.62973 (27256) *********************** 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 : 1.879 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: 1.5608 time to fit residues: 839.9640 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 : 2.061 ------------------------------------------------------------------------------- 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 198 optimal weight: 0.7980 chunk 178 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 0.0570 chunk 120 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 184 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 137 optimal weight: 1.9990 chunk 213 optimal weight: 0.6980 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 82 GLN ** 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.153126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.128825 restraints weight = 27991.761| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.17 r_work: 0.3588 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 19844 Z= 0.147 Angle : 0.596 11.113 27256 Z= 0.309 Chirality : 0.042 0.231 3067 Planarity : 0.005 0.114 3299 Dihedral : 16.723 133.018 3539 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.68 % Favored : 94.23 % Rotamer: Outliers : 5.74 % Allowed : 29.49 % Favored : 64.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.18), residues: 2288 helix: 1.34 (0.20), residues: 780 sheet: 1.14 (0.23), residues: 414 loop : -1.12 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 59 HIS 0.003 0.001 HIS J 6 PHE 0.015 0.001 PHE J 189 TYR 0.015 0.001 TYR I 265 ARG 0.008 0.001 ARG I 286 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 806) hydrogen bonds : angle 4.39929 ( 2299) covalent geometry : bond 0.00336 (19844) covalent geometry : angle 0.59576 (27256) *********************** 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 559 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 453 time to evaluate : 1.965 Fit side-chains revert: symmetry clash REVERT: F 63 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7841 (mtt-85) REVERT: F 103 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.6403 (pp-130) REVERT: F 127 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7534 (tm-30) REVERT: F 148 MET cc_start: 0.8009 (pp-130) cc_final: 0.7279 (pp-130) REVERT: F 209 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7841 (mtm) REVERT: F 278 ILE cc_start: 0.8398 (mm) cc_final: 0.8100 (mt) REVERT: F 310 ASP cc_start: 0.7981 (m-30) cc_final: 0.7752 (m-30) REVERT: H 218 TYR cc_start: 0.8550 (t80) cc_final: 0.8064 (t80) REVERT: H 256 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8089 (mttt) REVERT: I 111 LEU cc_start: 0.7676 (mm) cc_final: 0.7417 (mm) REVERT: I 150 GLU cc_start: 0.7396 (mp0) cc_final: 0.7073 (tt0) REVERT: J 168 GLU cc_start: 0.7538 (tp30) cc_final: 0.7272 (mp0) REVERT: J 272 GLU cc_start: 0.7442 (pt0) cc_final: 0.7137 (pt0) REVERT: J 274 LYS cc_start: 0.7525 (ptpt) cc_final: 0.7162 (pttt) REVERT: J 330 ASN cc_start: 0.7932 (t0) cc_final: 0.7467 (t0) REVERT: K 18 ARG cc_start: 0.7251 (mpt180) cc_final: 0.6877 (mpt180) REVERT: K 131 ASN cc_start: 0.8088 (OUTLIER) cc_final: 0.7724 (t0) REVERT: K 209 MET cc_start: 0.2560 (mmm) cc_final: 0.0900 (tmt) REVERT: K 246 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8102 (mp) REVERT: K 310 ASP cc_start: 0.7338 (m-30) cc_final: 0.7046 (m-30) REVERT: B 63 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7554 (OUTLIER) REVERT: B 78 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.7051 (mmt180) outliers start: 106 outliers final: 35 residues processed: 503 average time/residue: 1.2559 time to fit residues: 712.1112 Evaluate side-chains 458 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 416 time to evaluate : 1.990 ------------------------------------------------------------------------------- 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 278 ILE 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 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 79 optimal weight: 2.9990 chunk 23 optimal weight: 0.0170 chunk 139 optimal weight: 0.0010 chunk 55 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 219 optimal weight: 2.9990 overall best weight: 0.5224 ------------------------------------------------------------------------------- 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 86 ASN ** F 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN H 131 ASN H 164 ASN I 17 ASN I 127 GLN I 306 ASN J 17 ASN J 69 GLN J 86 ASN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 ASN K 131 ASN ** K 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 235 ASN K 349 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.152166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.128030 restraints weight = 27723.430| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.16 r_work: 0.3576 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 19844 Z= 0.134 Angle : 0.565 10.328 27256 Z= 0.292 Chirality : 0.041 0.208 3067 Planarity : 0.004 0.115 3299 Dihedral : 16.398 131.228 3491 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.68 % Favored : 94.23 % Rotamer: Outliers : 5.36 % Allowed : 29.27 % Favored : 65.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.18), residues: 2288 helix: 1.35 (0.19), residues: 780 sheet: 1.17 (0.24), residues: 417 loop : -1.08 (0.19), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 59 HIS 0.004 0.001 HIS I 180 PHE 0.017 0.001 PHE K 102 TYR 0.017 0.001 TYR I 265 ARG 0.009 0.000 ARG I 286 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 806) hydrogen bonds : angle 4.19476 ( 2299) covalent geometry : bond 0.00306 (19844) covalent geometry : angle 0.56521 (27256) *********************** 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 536 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 437 time to evaluate : 1.895 Fit side-chains revert: symmetry clash REVERT: F 52 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7198 (m-80) REVERT: F 63 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7732 (mtt-85) REVERT: F 127 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7553 (tm-30) REVERT: F 278 ILE cc_start: 0.8430 (mm) cc_final: 0.8199 (mt) REVERT: F 323 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7678 (mp) REVERT: H 122 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7497 (tm) REVERT: H 218 TYR cc_start: 0.8500 (t80) cc_final: 0.8135 (t80) REVERT: H 256 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8050 (mttt) REVERT: I 1 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8205 (ptm) REVERT: I 111 LEU cc_start: 0.7711 (mm) cc_final: 0.7458 (mm) REVERT: I 313 LEU cc_start: 0.8427 (mt) cc_final: 0.8219 (mt) REVERT: J 4 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7690 (mm-30) REVERT: J 168 GLU cc_start: 0.7497 (tp30) cc_final: 0.7249 (mp0) REVERT: J 251 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7842 (m) REVERT: K 4 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7906 (mt-10) REVERT: K 18 ARG cc_start: 0.7281 (mpt180) cc_final: 0.7007 (mpt180) REVERT: K 103 MET cc_start: 0.6465 (mmt) cc_final: 0.5610 (mmt) REVERT: K 131 ASN cc_start: 0.8003 (OUTLIER) cc_final: 0.7750 (t0) REVERT: K 209 MET cc_start: 0.2604 (mmm) cc_final: 0.0923 (tmt) REVERT: K 246 LEU cc_start: 0.8327 (mm) cc_final: 0.8117 (mp) REVERT: K 368 GLU cc_start: 0.7448 (pp20) cc_final: 0.6962 (pp20) REVERT: G 1 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7248 (ppp) REVERT: G 342 LEU cc_start: 0.1660 (OUTLIER) cc_final: 0.1239 (mp) REVERT: B 63 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7556 (mt) REVERT: B 68 MET cc_start: 0.7344 (ttt) cc_final: 0.6640 (ttt) REVERT: B 155 LEU cc_start: 0.8003 (tp) cc_final: 0.7785 (tt) outliers start: 99 outliers final: 40 residues processed: 489 average time/residue: 1.2595 time to fit residues: 696.1067 Evaluate side-chains 485 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 432 time to evaluate : 2.046 ------------------------------------------------------------------------------- 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 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 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 301 ILE Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 91 LYS 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 4 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 163 SER Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain K residue 4 GLU Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 105 LYS Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 26 THR 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 233 ASP 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 119 optimal weight: 0.0980 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 144 optimal weight: 0.0970 chunk 222 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 49 optimal weight: 0.0020 chunk 130 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 overall best weight: 0.3586 ------------------------------------------------------------------------------- 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 82 GLN F 180 HIS ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN H 131 ASN H 164 ASN I 17 ASN I 127 GLN I 306 ASN J 17 ASN J 69 GLN J 127 GLN K 17 ASN K 118 ASN K 131 ASN ** K 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 349 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.152809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.128620 restraints weight = 28055.364| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.17 r_work: 0.3585 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 19844 Z= 0.116 Angle : 0.551 10.206 27256 Z= 0.283 Chirality : 0.041 0.205 3067 Planarity : 0.004 0.115 3299 Dihedral : 16.272 125.860 3489 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.42 % Favored : 94.49 % Rotamer: Outliers : 5.57 % Allowed : 29.22 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.18), residues: 2288 helix: 1.35 (0.20), residues: 793 sheet: 1.21 (0.24), residues: 410 loop : -1.05 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 59 HIS 0.004 0.000 HIS I 180 PHE 0.017 0.001 PHE K 273 TYR 0.011 0.001 TYR I 315 ARG 0.008 0.000 ARG I 286 Details of bonding type rmsd hydrogen bonds : bond 0.03139 ( 806) hydrogen bonds : angle 4.02480 ( 2299) covalent geometry : bond 0.00265 (19844) covalent geometry : angle 0.55077 (27256) *********************** 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 549 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 446 time to evaluate : 1.885 Fit side-chains revert: symmetry clash REVERT: F 52 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7218 (m-80) REVERT: F 63 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7687 (mtt-85) REVERT: F 127 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7491 (tm-30) REVERT: F 278 ILE cc_start: 0.8461 (mm) cc_final: 0.8251 (mt) REVERT: F 323 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7689 (mp) REVERT: H 122 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7490 (tm) REVERT: H 359 ASP cc_start: 0.8053 (t70) cc_final: 0.7682 (t0) REVERT: I 87 LYS cc_start: 0.6765 (mtpt) cc_final: 0.6538 (mtmt) REVERT: I 111 LEU cc_start: 0.7705 (mm) cc_final: 0.7457 (mm) REVERT: I 313 LEU cc_start: 0.8426 (mt) cc_final: 0.8211 (mt) REVERT: J 4 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7595 (mm-30) REVERT: J 168 GLU cc_start: 0.7541 (tp30) cc_final: 0.7282 (mp0) REVERT: J 187 ASP cc_start: 0.7828 (t70) cc_final: 0.7586 (t70) REVERT: J 251 THR cc_start: 0.8097 (OUTLIER) cc_final: 0.7863 (m) REVERT: J 272 GLU cc_start: 0.7348 (pt0) cc_final: 0.6899 (pt0) REVERT: J 274 LYS cc_start: 0.7550 (ptpt) cc_final: 0.7073 (pttt) REVERT: K 4 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7877 (mt-10) REVERT: K 18 ARG cc_start: 0.7222 (mpt180) cc_final: 0.6562 (mpt180) REVERT: K 103 MET cc_start: 0.6168 (mmt) cc_final: 0.5351 (mmt) REVERT: K 131 ASN cc_start: 0.7900 (OUTLIER) cc_final: 0.7581 (t0) REVERT: K 368 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6994 (pp20) REVERT: G 1 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7226 (ppp) REVERT: G 342 LEU cc_start: 0.1644 (OUTLIER) cc_final: 0.1236 (mp) REVERT: G 345 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7696 (mtm110) REVERT: B 63 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7551 (mt) REVERT: B 68 MET cc_start: 0.7305 (ttt) cc_final: 0.6590 (ttt) REVERT: B 78 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.6928 (mmt180) outliers start: 103 outliers final: 43 residues processed: 498 average time/residue: 1.2329 time to fit residues: 694.0151 Evaluate side-chains 482 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 425 time to evaluate : 1.857 ------------------------------------------------------------------------------- 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 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 166 THR Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 256 LYS Chi-restraints excluded: chain H residue 301 ILE Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain 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 145 CYS Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain K residue 4 GLU Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 131 ASN 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 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 251 THR Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 247 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 106 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 200 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 82 GLN F 180 HIS ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN H 131 ASN H 164 ASN I 17 ASN I 127 GLN ** I 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 ASN J 69 GLN J 86 ASN J 127 GLN K 118 ASN K 131 ASN ** K 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 349 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.146153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.122038 restraints weight = 27833.443| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.16 r_work: 0.3495 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 19844 Z= 0.219 Angle : 0.637 9.532 27256 Z= 0.332 Chirality : 0.045 0.224 3067 Planarity : 0.004 0.117 3299 Dihedral : 16.636 120.769 3489 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.86 % Favored : 94.06 % Rotamer: Outliers : 6.17 % Allowed : 29.65 % Favored : 64.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.18), residues: 2288 helix: 1.14 (0.19), residues: 788 sheet: 0.92 (0.24), residues: 413 loop : -1.14 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 59 HIS 0.005 0.001 HIS J 239 PHE 0.027 0.002 PHE J 189 TYR 0.019 0.002 TYR I 265 ARG 0.011 0.001 ARG I 286 Details of bonding type rmsd hydrogen bonds : bond 0.03963 ( 806) hydrogen bonds : angle 4.38584 ( 2299) covalent geometry : bond 0.00501 (19844) covalent geometry : angle 0.63690 (27256) *********************** 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 558 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 444 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 52 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7415 (m-80) REVERT: F 63 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8094 (mtt-85) REVERT: F 103 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.6557 (pp-130) REVERT: F 209 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7857 (mtm) REVERT: H 74 GLU cc_start: 0.7580 (mp0) cc_final: 0.7295 (mp0) REVERT: H 103 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8547 (ttm) REVERT: H 122 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7414 (tm) REVERT: H 218 TYR cc_start: 0.8607 (t80) cc_final: 0.8283 (t80) REVERT: H 256 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8006 (mttt) REVERT: H 359 ASP cc_start: 0.8162 (t70) cc_final: 0.7803 (t0) REVERT: H 368 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6679 (pp20) REVERT: I 111 LEU cc_start: 0.7874 (mm) cc_final: 0.7654 (mm) REVERT: I 313 LEU cc_start: 0.8529 (mt) cc_final: 0.8302 (mt) REVERT: J 63 ARG cc_start: 0.8482 (ptp-170) cc_final: 0.8211 (ptp-170) REVERT: J 168 GLU cc_start: 0.7568 (tp30) cc_final: 0.7310 (mp0) REVERT: J 251 THR cc_start: 0.8087 (OUTLIER) cc_final: 0.7837 (m) REVERT: J 272 GLU cc_start: 0.7357 (pt0) cc_final: 0.7109 (pt0) REVERT: K 103 MET cc_start: 0.7159 (mmt) cc_final: 0.5851 (mmt) REVERT: K 131 ASN cc_start: 0.7844 (OUTLIER) cc_final: 0.7593 (t0) REVERT: K 209 MET cc_start: 0.2089 (mmm) cc_final: 0.0313 (tmt) REVERT: K 303 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.8018 (mt0) REVERT: K 368 GLU cc_start: 0.7535 (pp20) cc_final: 0.7072 (pp20) REVERT: G 1 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7186 (ppp) REVERT: G 342 LEU cc_start: 0.2195 (OUTLIER) cc_final: 0.1791 (mp) REVERT: G 345 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7685 (mtm110) REVERT: B 54 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.6119 (mp0) REVERT: B 68 MET cc_start: 0.7415 (ttt) cc_final: 0.6716 (ttt) outliers start: 114 outliers final: 59 residues processed: 503 average time/residue: 1.2098 time to fit residues: 689.4958 Evaluate side-chains 496 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 422 time to evaluate : 1.941 ------------------------------------------------------------------------------- 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 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 103 MET 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 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 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 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 181 ILE Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 131 ASN 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 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 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 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 164 LEU 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 162 optimal weight: 0.0570 chunk 214 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 204 optimal weight: 0.9990 chunk 89 optimal weight: 0.0370 chunk 100 optimal weight: 0.7980 chunk 191 optimal weight: 7.9990 chunk 215 optimal weight: 0.1980 chunk 58 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- 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 306 ASN H 17 ASN H 86 ASN H 164 ASN H 370 GLN I 17 ASN I 127 GLN I 152 ASN ** I 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 ASN J 69 GLN J 127 GLN J 349 ASN K 118 ASN K 131 ASN ** K 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 235 ASN K 349 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.149479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.125496 restraints weight = 28039.555| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.17 r_work: 0.3544 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 19844 Z= 0.122 Angle : 0.577 9.924 27256 Z= 0.295 Chirality : 0.041 0.222 3067 Planarity : 0.004 0.114 3299 Dihedral : 16.302 110.366 3485 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.20 % Favored : 94.71 % Rotamer: Outliers : 4.82 % Allowed : 30.57 % Favored : 64.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.18), residues: 2288 helix: 1.37 (0.20), residues: 782 sheet: 0.85 (0.23), residues: 428 loop : -1.09 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP F 78 HIS 0.003 0.001 HIS I 180 PHE 0.013 0.001 PHE K 273 TYR 0.020 0.001 TYR I 265 ARG 0.010 0.000 ARG I 286 Details of bonding type rmsd hydrogen bonds : bond 0.03193 ( 806) hydrogen bonds : angle 4.09111 ( 2299) covalent geometry : bond 0.00280 (19844) covalent geometry : angle 0.57702 (27256) *********************** 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 529 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 440 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 52 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7214 (m-80) REVERT: F 63 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7637 (mtt-85) REVERT: F 323 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7832 (mp) REVERT: H 122 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7413 (tm) REVERT: H 127 GLN cc_start: 0.7757 (tp40) cc_final: 0.7523 (tp-100) REVERT: H 218 TYR cc_start: 0.8567 (t80) cc_final: 0.8224 (t80) REVERT: H 359 ASP cc_start: 0.8111 (t70) cc_final: 0.7718 (t0) REVERT: H 368 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6659 (pp20) REVERT: I 111 LEU cc_start: 0.7793 (mm) cc_final: 0.7572 (mm) REVERT: I 313 LEU cc_start: 0.8479 (mt) cc_final: 0.8244 (mt) REVERT: J 102 PHE cc_start: 0.8442 (t80) cc_final: 0.8204 (t80) REVERT: J 168 GLU cc_start: 0.7512 (tp30) cc_final: 0.7288 (mp0) REVERT: J 251 THR cc_start: 0.8057 (OUTLIER) cc_final: 0.7803 (m) REVERT: J 272 GLU cc_start: 0.7319 (pt0) cc_final: 0.7101 (pt0) REVERT: K 18 ARG cc_start: 0.7272 (mpt180) cc_final: 0.6951 (mpt180) REVERT: K 103 MET cc_start: 0.6533 (mmt) cc_final: 0.5525 (mmt) REVERT: K 131 ASN cc_start: 0.7725 (OUTLIER) cc_final: 0.7504 (t0) REVERT: K 240 THR cc_start: 0.8420 (m) cc_final: 0.8210 (m) REVERT: K 368 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7081 (pp20) REVERT: G 1 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7218 (ppp) REVERT: G 342 LEU cc_start: 0.2197 (OUTLIER) cc_final: 0.1782 (mp) REVERT: G 345 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7704 (mtm110) REVERT: B 54 GLU cc_start: 0.6304 (OUTLIER) cc_final: 0.6028 (mp0) REVERT: B 68 MET cc_start: 0.7297 (ttt) cc_final: 0.6562 (ttt) REVERT: B 78 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.7008 (mmt180) outliers start: 89 outliers final: 43 residues processed: 484 average time/residue: 1.2720 time to fit residues: 698.1257 Evaluate side-chains 480 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 424 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 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 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 224 GLU Chi-restraints excluded: chain H residue 256 LYS Chi-restraints excluded: chain H residue 368 GLU 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 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 137 THR Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain K residue 297 VAL 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 148 MET Chi-restraints excluded: chain G residue 172 GLN Chi-restraints excluded: chain G residue 212 SER Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 247 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 147 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 190 optimal weight: 6.9990 chunk 10 optimal weight: 0.0980 chunk 60 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 68 optimal weight: 0.2980 chunk 104 optimal weight: 0.3980 chunk 85 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 50 ASN F 82 GLN F 127 GLN H 17 ASN H 86 ASN H 164 ASN H 257 GLN H 299 GLN I 17 ASN I 127 GLN ** I 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 ASN J 69 GLN J 86 ASN K 131 ASN K 175 HIS ** K 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.148598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.124524 restraints weight = 27772.309| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.16 r_work: 0.3541 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 19844 Z= 0.127 Angle : 0.574 9.438 27256 Z= 0.295 Chirality : 0.041 0.211 3067 Planarity : 0.004 0.114 3299 Dihedral : 16.209 107.339 3485 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.86 % Favored : 94.06 % Rotamer: Outliers : 4.55 % Allowed : 31.28 % Favored : 64.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.18), residues: 2288 helix: 1.39 (0.19), residues: 785 sheet: 0.92 (0.24), residues: 425 loop : -1.05 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP F 78 HIS 0.003 0.001 HIS G 180 PHE 0.019 0.001 PHE K 273 TYR 0.016 0.001 TYR I 316 ARG 0.010 0.000 ARG I 286 Details of bonding type rmsd hydrogen bonds : bond 0.03160 ( 806) hydrogen bonds : angle 4.05298 ( 2299) covalent geometry : bond 0.00290 (19844) covalent geometry : angle 0.57386 (27256) *********************** 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 512 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 428 time to evaluate : 1.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 52 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7167 (m-80) REVERT: F 63 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7744 (mtt-85) REVERT: F 70 GLN cc_start: 0.7629 (tt0) cc_final: 0.7422 (tt0) REVERT: F 127 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7395 (tm-30) REVERT: F 147 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7609 (ptt90) REVERT: F 310 ASP cc_start: 0.8054 (m-30) cc_final: 0.7845 (m-30) REVERT: F 323 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7761 (mp) REVERT: H 122 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7469 (tm) REVERT: H 218 TYR cc_start: 0.8556 (t80) cc_final: 0.8245 (t80) REVERT: H 256 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8029 (mttt) REVERT: H 359 ASP cc_start: 0.8095 (t70) cc_final: 0.7708 (t0) REVERT: H 368 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6667 (pp20) REVERT: I 111 LEU cc_start: 0.7780 (mm) cc_final: 0.7556 (mm) REVERT: I 138 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7661 (tp) REVERT: I 313 LEU cc_start: 0.8487 (mt) cc_final: 0.8246 (mt) REVERT: J 4 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7847 (mm-30) REVERT: J 168 GLU cc_start: 0.7535 (tp30) cc_final: 0.7306 (mp0) REVERT: J 251 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7862 (m) REVERT: J 272 GLU cc_start: 0.7380 (pt0) cc_final: 0.7121 (pt0) REVERT: K 18 ARG cc_start: 0.7273 (mpt180) cc_final: 0.6992 (mpt180) REVERT: K 34 ARG cc_start: 0.8225 (mpt-90) cc_final: 0.8010 (mtt180) REVERT: K 103 MET cc_start: 0.6519 (mmt) cc_final: 0.5468 (mmt) REVERT: K 131 ASN cc_start: 0.7803 (OUTLIER) cc_final: 0.7564 (t0) REVERT: K 209 MET cc_start: 0.1804 (mmm) cc_final: 0.0100 (tmt) REVERT: K 286 ARG cc_start: 0.8450 (mmm160) cc_final: 0.8213 (mmm160) REVERT: K 368 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7075 (pp20) REVERT: G 1 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7123 (ppp) REVERT: G 34 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.6875 (mtt180) REVERT: G 209 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7878 (mmm) REVERT: G 345 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7698 (mtm110) REVERT: B 54 GLU cc_start: 0.6298 (OUTLIER) cc_final: 0.6021 (mp0) REVERT: B 68 MET cc_start: 0.7266 (ttt) cc_final: 0.6572 (ttt) outliers start: 84 outliers final: 47 residues processed: 467 average time/residue: 1.2043 time to fit residues: 638.3878 Evaluate side-chains 500 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 435 time to evaluate : 2.012 ------------------------------------------------------------------------------- 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 127 GLN Chi-restraints excluded: chain F residue 147 ARG 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 166 THR 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 113 ARG Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 166 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 J residue 4 GLU Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 103 MET Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain K residue 297 VAL 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 34 ARG Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 172 GLN Chi-restraints excluded: chain G residue 209 MET Chi-restraints excluded: chain G residue 212 SER Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 17 GLN 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 193 VAL Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 247 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 113 optimal weight: 0.0670 chunk 175 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 230 optimal weight: 0.3980 chunk 110 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.5720 ------------------------------------------------------------------------------- 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 50 ASN F 127 GLN ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN H 164 ASN I 17 ASN I 127 GLN ** I 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 ASN J 69 GLN K 131 ASN ** K 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.147809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.123755 restraints weight = 27832.473| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.16 r_work: 0.3526 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2545 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= 0.140 Angle : 0.586 9.171 27256 Z= 0.301 Chirality : 0.042 0.215 3067 Planarity : 0.004 0.113 3299 Dihedral : 16.189 102.642 3485 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.81 % Favored : 94.10 % Rotamer: Outliers : 4.65 % Allowed : 31.71 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.18), residues: 2288 helix: 1.35 (0.19), residues: 785 sheet: 0.91 (0.24), residues: 417 loop : -1.03 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP B 59 HIS 0.003 0.001 HIS J 204 PHE 0.020 0.001 PHE J 189 TYR 0.017 0.001 TYR I 265 ARG 0.010 0.000 ARG I 286 Details of bonding type rmsd hydrogen bonds : bond 0.03246 ( 806) hydrogen bonds : angle 4.07111 ( 2299) covalent geometry : bond 0.00322 (19844) covalent geometry : angle 0.58604 (27256) *********************** 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 523 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 437 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 52 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7327 (m-80) REVERT: F 63 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7747 (mtt-85) REVERT: F 70 GLN cc_start: 0.7641 (tt0) cc_final: 0.7410 (tt0) REVERT: F 127 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7375 (tm-30) REVERT: F 147 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7645 (ptt90) REVERT: F 250 LYS cc_start: 0.8414 (mtmm) cc_final: 0.8095 (mtmm) REVERT: F 310 ASP cc_start: 0.8081 (m-30) cc_final: 0.7851 (m-30) REVERT: H 122 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7483 (tm) REVERT: H 218 TYR cc_start: 0.8550 (t80) cc_final: 0.8251 (t80) REVERT: H 251 THR cc_start: 0.8528 (p) cc_final: 0.8266 (t) REVERT: H 256 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7964 (mttt) REVERT: H 359 ASP cc_start: 0.8096 (t70) cc_final: 0.7718 (t0) REVERT: H 368 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6632 (pp20) REVERT: I 111 LEU cc_start: 0.7784 (mm) cc_final: 0.7569 (mm) REVERT: I 138 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7669 (tp) REVERT: I 313 LEU cc_start: 0.8484 (mt) cc_final: 0.8220 (mt) REVERT: J 168 GLU cc_start: 0.7537 (tp30) cc_final: 0.7317 (mp0) REVERT: J 251 THR cc_start: 0.8108 (OUTLIER) cc_final: 0.7855 (m) REVERT: J 272 GLU cc_start: 0.7378 (pt0) cc_final: 0.7117 (pt0) REVERT: K 18 ARG cc_start: 0.7281 (mpt180) cc_final: 0.6954 (mpt180) REVERT: K 82 GLN cc_start: 0.7872 (mm-40) cc_final: 0.7249 (mt0) REVERT: K 103 MET cc_start: 0.6671 (mmt) cc_final: 0.5538 (mmt) REVERT: K 209 MET cc_start: 0.1821 (mmm) cc_final: 0.0065 (tmt) REVERT: K 286 ARG cc_start: 0.8455 (mmm160) cc_final: 0.8210 (mmm160) REVERT: K 368 GLU cc_start: 0.7529 (pp20) cc_final: 0.7087 (pp20) REVERT: G 1 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7136 (ppp) REVERT: G 34 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.6901 (mtt180) REVERT: G 209 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7831 (mtp) REVERT: G 345 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7712 (mtm110) REVERT: B 54 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.6031 (mp0) REVERT: B 68 MET cc_start: 0.7251 (ttt) cc_final: 0.6523 (ttt) outliers start: 86 outliers final: 52 residues processed: 475 average time/residue: 1.2310 time to fit residues: 660.6712 Evaluate side-chains 501 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 435 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 147 ARG 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 166 THR 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 293 GLU Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 138 LEU 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 J residue 53 LYS Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 181 ILE 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 26 THR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 34 ARG Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 172 GLN Chi-restraints excluded: chain G residue 209 MET Chi-restraints excluded: chain G residue 212 SER Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 17 GLN 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 193 VAL Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 247 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 134 optimal weight: 8.9990 chunk 124 optimal weight: 0.9980 chunk 228 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 219 optimal weight: 0.3980 chunk 120 optimal weight: 0.7980 chunk 204 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 181 optimal weight: 0.0770 chunk 35 optimal weight: 0.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- 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 50 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 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 349 ASN J 17 ASN J 69 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.147331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.123614 restraints weight = 27879.653| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.34 r_work: 0.3504 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2621 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= 0.151 Angle : 0.599 10.466 27256 Z= 0.307 Chirality : 0.042 0.216 3067 Planarity : 0.004 0.112 3299 Dihedral : 16.175 100.461 3485 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.94 % Favored : 93.97 % Rotamer: Outliers : 4.33 % Allowed : 32.09 % Favored : 63.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.18), residues: 2288 helix: 1.32 (0.19), residues: 785 sheet: 0.88 (0.24), residues: 421 loop : -1.06 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP B 59 HIS 0.003 0.001 HIS J 204 PHE 0.023 0.001 PHE J 189 TYR 0.019 0.001 TYR I 265 ARG 0.010 0.000 ARG I 286 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 806) hydrogen bonds : angle 4.11198 ( 2299) covalent geometry : bond 0.00346 (19844) covalent geometry : angle 0.59866 (27256) *********************** 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 517 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 437 time to evaluate : 1.922 Fit side-chains revert: symmetry clash REVERT: F 52 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.7355 (m-80) REVERT: F 63 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7743 (mtt-85) REVERT: F 70 GLN cc_start: 0.7643 (tt0) cc_final: 0.7400 (tt0) REVERT: F 82 GLN cc_start: 0.7756 (mt0) cc_final: 0.7507 (tt0) REVERT: F 147 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7651 (ptt90) REVERT: F 250 LYS cc_start: 0.8436 (mtmm) cc_final: 0.8099 (mtmm) REVERT: H 122 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7503 (tm) REVERT: H 218 TYR cc_start: 0.8574 (t80) cc_final: 0.8276 (t80) REVERT: H 251 THR cc_start: 0.8547 (p) cc_final: 0.8287 (t) REVERT: H 256 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7975 (mttt) REVERT: H 359 ASP cc_start: 0.8135 (t70) cc_final: 0.7755 (t0) REVERT: H 368 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6623 (pp20) REVERT: I 111 LEU cc_start: 0.7794 (mm) cc_final: 0.7579 (mm) REVERT: I 138 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7760 (tp) REVERT: I 313 LEU cc_start: 0.8503 (mt) cc_final: 0.8260 (mt) REVERT: J 103 MET cc_start: 0.7988 (ppp) cc_final: 0.7641 (ptp) REVERT: J 168 GLU cc_start: 0.7607 (tp30) cc_final: 0.7381 (mp0) REVERT: J 251 THR cc_start: 0.8133 (OUTLIER) cc_final: 0.7879 (m) REVERT: J 274 LYS cc_start: 0.7777 (ptpt) cc_final: 0.7541 (ptpt) REVERT: K 18 ARG cc_start: 0.7289 (mpt180) cc_final: 0.6926 (mpt180) REVERT: K 82 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7258 (mt0) REVERT: K 103 MET cc_start: 0.6824 (mmt) cc_final: 0.5538 (mmt) REVERT: K 209 MET cc_start: 0.1698 (mmm) cc_final: -0.0031 (tmt) REVERT: K 368 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7173 (pp20) REVERT: K 370 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7626 (mp10) REVERT: G 1 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7150 (ppp) REVERT: G 34 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.6902 (mtt180) REVERT: G 209 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7937 (mmm) REVERT: G 345 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7737 (mtm110) REVERT: B 54 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.6064 (mp0) REVERT: B 68 MET cc_start: 0.7250 (ttt) cc_final: 0.6547 (ttt) outliers start: 80 outliers final: 57 residues processed: 476 average time/residue: 1.2983 time to fit residues: 709.5512 Evaluate side-chains 503 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 432 time to evaluate : 2.185 ------------------------------------------------------------------------------- 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 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 166 THR 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 293 GLU Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 138 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 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 J residue 53 LYS Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 181 ILE Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 299 GLN Chi-restraints excluded: chain K residue 309 ASN Chi-restraints excluded: chain K residue 323 ILE 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 34 ARG Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 172 GLN Chi-restraints excluded: chain G residue 209 MET Chi-restraints excluded: chain G residue 212 SER Chi-restraints excluded: chain G residue 221 ILE Chi-restraints excluded: chain G residue 236 LEU 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 17 GLN 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 193 VAL Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 247 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 145 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 65 optimal weight: 0.2980 chunk 70 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 0.0870 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 50 ASN F 82 GLN F 127 GLN F 131 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 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 ASN J 69 GLN ** K 225 GLN ** 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 = 0.3950 r_free = 0.3950 target = 0.149633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.126028 restraints weight = 27781.862| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.13 r_work: 0.3525 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2705 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= 0.133 Angle : 0.591 9.469 27256 Z= 0.303 Chirality : 0.041 0.216 3067 Planarity : 0.004 0.111 3299 Dihedral : 16.091 99.164 3485 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.68 % Favored : 94.23 % Rotamer: Outliers : 4.00 % Allowed : 32.58 % Favored : 63.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.18), residues: 2288 helix: 1.36 (0.19), residues: 791 sheet: 0.86 (0.24), residues: 431 loop : -1.06 (0.20), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP B 59 HIS 0.003 0.001 HIS J 204 PHE 0.020 0.001 PHE J 189 TYR 0.015 0.001 TYR I 265 ARG 0.010 0.000 ARG I 286 Details of bonding type rmsd hydrogen bonds : bond 0.03161 ( 806) hydrogen bonds : angle 4.04783 ( 2299) covalent geometry : bond 0.00307 (19844) covalent geometry : angle 0.59124 (27256) ********************** 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 502 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 428 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 52 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7224 (m-80) REVERT: F 63 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7593 (mtt-85) REVERT: F 70 GLN cc_start: 0.7611 (tt0) cc_final: 0.7370 (tt0) REVERT: F 86 ASN cc_start: 0.7925 (m-40) cc_final: 0.7589 (m-40) REVERT: F 107 LYS cc_start: 0.7472 (tppp) cc_final: 0.7026 (tppp) REVERT: F 147 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7616 (ptt90) REVERT: F 250 LYS cc_start: 0.8391 (mtmm) cc_final: 0.8071 (mtmm) REVERT: F 310 ASP cc_start: 0.8041 (m-30) cc_final: 0.7835 (m-30) REVERT: H 122 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7469 (tm) REVERT: H 218 TYR cc_start: 0.8562 (t80) cc_final: 0.8254 (t80) REVERT: H 251 THR cc_start: 0.8493 (p) cc_final: 0.8240 (t) REVERT: H 256 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7988 (mttt) REVERT: H 359 ASP cc_start: 0.8070 (t70) cc_final: 0.7673 (t0) REVERT: H 368 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6600 (pp20) REVERT: I 111 LEU cc_start: 0.7743 (mm) cc_final: 0.7538 (mm) REVERT: I 138 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7698 (tp) REVERT: I 313 LEU cc_start: 0.8488 (mt) cc_final: 0.8229 (mt) REVERT: J 4 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7647 (mm-30) REVERT: J 103 MET cc_start: 0.7943 (ppp) cc_final: 0.7598 (ptp) REVERT: J 168 GLU cc_start: 0.7536 (tp30) cc_final: 0.7309 (mp0) REVERT: J 251 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7863 (m) REVERT: J 272 GLU cc_start: 0.7394 (pt0) cc_final: 0.7125 (pt0) REVERT: K 18 ARG cc_start: 0.7259 (mpt180) cc_final: 0.6958 (mpt180) REVERT: K 103 MET cc_start: 0.6681 (mmt) cc_final: 0.5391 (mmt) REVERT: K 368 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7108 (pp20) REVERT: G 1 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7157 (ppp) REVERT: G 34 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.6899 (mtt180) REVERT: G 209 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7703 (mtm) REVERT: G 345 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7732 (mtm110) REVERT: B 54 GLU cc_start: 0.6336 (OUTLIER) cc_final: 0.6067 (mp0) REVERT: B 68 MET cc_start: 0.7197 (ttt) cc_final: 0.6470 (ttt) outliers start: 74 outliers final: 50 residues processed: 462 average time/residue: 1.2616 time to fit residues: 658.0210 Evaluate side-chains 486 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 422 time to evaluate : 1.934 ------------------------------------------------------------------------------- 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 82 GLN Chi-restraints excluded: chain F residue 147 ARG 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 166 THR Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 256 LYS Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 138 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 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 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 137 THR 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 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 299 GLN Chi-restraints excluded: chain K residue 323 ILE 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 34 ARG Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 209 MET Chi-restraints excluded: chain G residue 212 SER Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 17 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 76 optimal weight: 0.0020 chunk 209 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 190 optimal weight: 0.0980 chunk 210 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 176 optimal weight: 0.0270 overall best weight: 1.0250 ------------------------------------------------------------------------------- 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 50 ASN F 82 GLN F 127 GLN ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN H 131 ASN H 164 ASN H 225 GLN I 127 GLN ** I 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 349 ASN J 17 ASN J 69 GLN J 70 GLN ** K 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.144814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.120936 restraints weight = 27809.336| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.15 r_work: 0.3480 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 19844 Z= 0.202 Angle : 0.648 11.630 27256 Z= 0.333 Chirality : 0.044 0.236 3067 Planarity : 0.004 0.111 3299 Dihedral : 16.219 100.558 3480 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.08 % Favored : 93.84 % Rotamer: Outliers : 4.06 % Allowed : 32.31 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.18), residues: 2288 helix: 1.31 (0.19), residues: 779 sheet: 0.77 (0.24), residues: 422 loop : -1.13 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 59 HIS 0.004 0.001 HIS J 239 PHE 0.031 0.002 PHE J 189 TYR 0.020 0.002 TYR I 265 ARG 0.011 0.000 ARG I 286 Details of bonding type rmsd hydrogen bonds : bond 0.03699 ( 806) hydrogen bonds : angle 4.25650 ( 2299) covalent geometry : bond 0.00465 (19844) covalent geometry : angle 0.64783 (27256) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17451.07 seconds wall clock time: 298 minutes 14.39 seconds (17894.39 seconds total)