Starting phenix.real_space_refine on Sun Sep 13 17:06:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vqv_21358/09_2026/6vqv_21358.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vqv_21358/09_2026/6vqv_21358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vqv_21358/09_2026/6vqv_21358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vqv_21358/09_2026/6vqv_21358.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6vqv_21358/09_2026/6vqv_21358.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vqv_21358/09_2026/6vqv_21358.cif" model { file = "/net/cci-nas-00/data/ceres_data/6vqv_21358/09_2026/6vqv_21358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vqv_21358/09_2026/6vqv_21358.cif" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 60 5.49 5 S 33 5.16 5 C 15268 2.51 5 N 4514 2.21 5 O 4801 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24676 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 545 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "B" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 545 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "C" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3378 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 24, 'TRANS': 397} Chain: "D" Number of atoms: 2410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2410 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 23, 'TRANS': 282} Chain breaks: 1 Chain: "E" Number of atoms: 2204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2204 Classifications: {'peptide': 285} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 273} Chain breaks: 2 Chain: "F" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2541 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 Chain: "G" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2532 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain breaks: 1 Chain: "H" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "I" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2532 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain breaks: 1 Chain: "J" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2611 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "K" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1511 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 15, 'TRANS': 171} Chain: "L" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1275 Classifications: {'RNAv2': 60} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 12, 'rna3p_pur': 20, 'rna3p_pyr': 19} Link IDs: {'rna2p': 20, 'rna3p': 39} Time building chain proxies: 5.45, per 1000 atoms: 0.22 Number of scatterers: 24676 At special positions: 0 Unit cell: (151.45, 141.05, 150.15, 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 33 16.00 P 60 15.00 O 4801 8.00 N 4514 7.00 C 15268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 1.1 seconds 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5564 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 41 sheets defined 24.8% alpha, 21.6% beta 0 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 3.32 Creating SS restraints... Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'B' and resid 26 through 36 Processing helix chain 'C' and resid 115 through 126 removed outlier: 3.807A pdb=" N LYS C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU C 123 " --> pdb=" O LYS C 119 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLN C 124 " --> pdb=" O PHE C 120 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TYR C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 203 Processing helix chain 'C' and resid 204 through 206 No H-bonds generated for 'chain 'C' and resid 204 through 206' Processing helix chain 'C' and resid 212 through 224 removed outlier: 3.584A pdb=" N ALA C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 342 removed outlier: 4.286A pdb=" N ARG C 321 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL C 326 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C 327 " --> pdb=" O ALA C 323 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 334 " --> pdb=" O CYS C 330 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 386 removed outlier: 4.006A pdb=" N GLU C 386 " --> pdb=" O TRP C 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 383 through 386' Processing helix chain 'C' and resid 387 through 397 removed outlier: 3.743A pdb=" N TRP C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN C 396 " --> pdb=" O ALA C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 421 removed outlier: 3.580A pdb=" N SER C 415 " --> pdb=" O ALA C 411 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU C 417 " --> pdb=" O GLN C 413 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU C 418 " --> pdb=" O TRP C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 430 Processing helix chain 'D' and resid 33 through 46 removed outlier: 3.992A pdb=" N PHE D 37 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS D 42 " --> pdb=" O THR D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 119 removed outlier: 3.793A pdb=" N LEU D 118 " --> pdb=" O GLY D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 132 removed outlier: 3.571A pdb=" N ILE D 126 " --> pdb=" O PRO D 122 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG D 128 " --> pdb=" O GLN D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'D' and resid 189 through 196 removed outlier: 4.153A pdb=" N LEU D 193 " --> pdb=" O ARG D 189 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN D 194 " --> pdb=" O GLU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 212 removed outlier: 3.543A pdb=" N LEU D 210 " --> pdb=" O GLU D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 302 removed outlier: 3.749A pdb=" N LEU D 302 " --> pdb=" O SER D 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 147 Processing helix chain 'E' and resid 149 through 162 removed outlier: 3.560A pdb=" N ARG E 155 " --> pdb=" O GLU E 151 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN E 162 " --> pdb=" O HIS E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 223 Processing helix chain 'E' and resid 274 through 279 Processing helix chain 'E' and resid 280 through 282 No H-bonds generated for 'chain 'E' and resid 280 through 282' Processing helix chain 'E' and resid 321 through 331 removed outlier: 3.684A pdb=" N TRP E 329 " --> pdb=" O LEU E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 351 Processing helix chain 'F' and resid 81 through 89 removed outlier: 3.856A pdb=" N ASP F 86 " --> pdb=" O PRO F 82 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ALA F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N SER F 88 " --> pdb=" O LYS F 84 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE F 89 " --> pdb=" O LEU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 147 removed outlier: 3.662A pdb=" N ARG F 133 " --> pdb=" O ASP F 129 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN F 145 " --> pdb=" O ALA F 141 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP F 146 " --> pdb=" O THR F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 162 removed outlier: 3.629A pdb=" N HIS F 158 " --> pdb=" O ARG F 154 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN F 159 " --> pdb=" O ARG F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 222 removed outlier: 3.705A pdb=" N LEU F 216 " --> pdb=" O ALA F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 283 Processing helix chain 'F' and resid 321 through 331 Processing helix chain 'F' and resid 337 through 351 removed outlier: 3.971A pdb=" N HIS F 342 " --> pdb=" O VAL F 338 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR F 343 " --> pdb=" O GLU F 339 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY F 351 " --> pdb=" O ASN F 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 90 Processing helix chain 'G' and resid 129 through 147 removed outlier: 3.794A pdb=" N ARG G 133 " --> pdb=" O ASP G 129 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS G 135 " --> pdb=" O ALA G 131 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN G 138 " --> pdb=" O ASP G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 162 removed outlier: 4.090A pdb=" N ARG G 155 " --> pdb=" O GLU G 151 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS G 158 " --> pdb=" O ARG G 154 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN G 159 " --> pdb=" O ARG G 155 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU G 160 " --> pdb=" O TYR G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 200 Processing helix chain 'G' and resid 209 through 222 removed outlier: 3.658A pdb=" N LEU G 213 " --> pdb=" O GLU G 209 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU G 216 " --> pdb=" O ALA G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 283 Processing helix chain 'G' and resid 321 through 331 removed outlier: 3.622A pdb=" N TRP G 329 " --> pdb=" O LEU G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 350 removed outlier: 3.632A pdb=" N HIS G 342 " --> pdb=" O VAL G 338 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR G 343 " --> pdb=" O GLU G 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 54 removed outlier: 3.778A pdb=" N ARG H 51 " --> pdb=" O TRP H 48 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASP H 52 " --> pdb=" O ALA H 49 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER H 54 " --> pdb=" O ARG H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 90 removed outlier: 3.852A pdb=" N LEU H 85 " --> pdb=" O ASP H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 147 removed outlier: 3.579A pdb=" N ASP H 146 " --> pdb=" O THR H 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 162 removed outlier: 3.514A pdb=" N HIS H 158 " --> pdb=" O ARG H 154 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN H 159 " --> pdb=" O ARG H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 222 removed outlier: 3.589A pdb=" N LEU H 213 " --> pdb=" O GLU H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 276 through 281 Processing helix chain 'H' and resid 321 through 331 removed outlier: 3.699A pdb=" N ASN H 328 " --> pdb=" O THR H 324 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 351 removed outlier: 3.627A pdb=" N TYR H 343 " --> pdb=" O GLU H 339 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE H 345 " --> pdb=" O GLN H 341 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 57 removed outlier: 3.556A pdb=" N ALA I 53 " --> pdb=" O GLN I 50 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER I 54 " --> pdb=" O ARG I 51 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLN I 55 " --> pdb=" O ASP I 52 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU I 56 " --> pdb=" O ALA I 53 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TRP I 57 " --> pdb=" O SER I 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 50 through 57' Processing helix chain 'I' and resid 81 through 91 removed outlier: 4.033A pdb=" N ALA I 87 " --> pdb=" O ALA I 83 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER I 91 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 147 Processing helix chain 'I' and resid 149 through 162 Processing helix chain 'I' and resid 209 through 222 removed outlier: 3.818A pdb=" N LEU I 213 " --> pdb=" O GLU I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 281 Processing helix chain 'I' and resid 321 through 331 Processing helix chain 'I' and resid 337 through 351 removed outlier: 3.733A pdb=" N HIS I 342 " --> pdb=" O VAL I 338 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR I 343 " --> pdb=" O GLU I 339 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY I 351 " --> pdb=" O ASN I 347 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 57 removed outlier: 4.460A pdb=" N GLU J 56 " --> pdb=" O ALA J 53 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP J 57 " --> pdb=" O SER J 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 53 through 57' Processing helix chain 'J' and resid 81 through 87 Processing helix chain 'J' and resid 129 through 145 removed outlier: 3.525A pdb=" N GLN J 138 " --> pdb=" O ASP J 134 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR J 139 " --> pdb=" O LYS J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 162 removed outlier: 3.625A pdb=" N ARG J 155 " --> pdb=" O GLU J 151 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN J 159 " --> pdb=" O ARG J 155 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU J 160 " --> pdb=" O TYR J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 223 removed outlier: 3.955A pdb=" N ALA J 212 " --> pdb=" O ALA J 208 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU J 213 " --> pdb=" O GLU J 209 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY J 223 " --> pdb=" O SER J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 274 through 283 Processing helix chain 'J' and resid 321 through 331 removed outlier: 4.207A pdb=" N ASP J 327 " --> pdb=" O TYR J 323 " (cutoff:3.500A) Processing helix chain 'J' and resid 337 through 350 removed outlier: 3.520A pdb=" N TYR J 343 " --> pdb=" O GLU J 339 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 69 removed outlier: 4.216A pdb=" N ARG K 68 " --> pdb=" O ALA K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 73 removed outlier: 4.396A pdb=" N ARG K 73 " --> pdb=" O LEU K 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 70 through 73' Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 24 removed outlier: 3.594A pdb=" N TYR A 5 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET A 45 " --> pdb=" O TYR A 57 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N TYR A 57 " --> pdb=" O MET A 45 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE A 47 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 20 through 24 removed outlier: 3.595A pdb=" N TYR B 5 " --> pdb=" O ILE B 22 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET B 45 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N TYR B 57 " --> pdb=" O MET B 45 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE B 47 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 65 through 66 Processing sheet with id=AA4, first strand: chain 'C' and resid 68 through 69 Processing sheet with id=AA5, first strand: chain 'C' and resid 178 through 181 removed outlier: 5.098A pdb=" N ILE D 61 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N SER D 188 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 13.520A pdb=" N VAL D 59 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL D 59 " --> pdb=" O GLY D 112 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLY D 112 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE D 61 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU D 110 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N CYS D 63 " --> pdb=" O SER D 108 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N SER D 108 " --> pdb=" O CYS D 63 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG D 65 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA D 103 " --> pdb=" O GLN D 18 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLN D 18 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU D 105 " --> pdb=" O SER D 16 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER D 16 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N VAL D 107 " --> pdb=" O ARG D 14 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARG D 14 " --> pdb=" O VAL D 107 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU D 11 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA D 157 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 143 through 145 removed outlier: 4.277A pdb=" N SER D 16 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARG D 14 " --> pdb=" O VAL D 107 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N VAL D 107 " --> pdb=" O ARG D 14 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER D 16 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU D 105 " --> pdb=" O SER D 16 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLN D 18 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA D 103 " --> pdb=" O GLN D 18 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG D 65 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N SER D 108 " --> pdb=" O CYS D 63 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N CYS D 63 " --> pdb=" O SER D 108 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU D 110 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE D 61 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLY D 112 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL D 59 " --> pdb=" O GLY D 112 " (cutoff:3.500A) removed outlier: 13.520A pdb=" N VAL D 59 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N SER D 188 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ILE D 61 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N PHE D 279 " --> pdb=" O ALA D 257 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ALA D 257 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLU D 281 " --> pdb=" O TYR D 255 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR D 255 " --> pdb=" O GLU D 281 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU D 283 " --> pdb=" O ALA D 253 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TRP D 247 " --> pdb=" O TRP D 289 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ALA D 253 " --> pdb=" O TRP D 316 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP D 316 " --> pdb=" O ALA D 253 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 30 removed outlier: 4.681A pdb=" N PHE D 81 " --> pdb=" O ILE C 240 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N LYS C 242 " --> pdb=" O PHE D 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 219 through 220 Processing sheet with id=AA9, first strand: chain 'E' and resid 31 through 32 Processing sheet with id=AB1, first strand: chain 'E' and resid 37 through 38 removed outlier: 3.558A pdb=" N ALA E 235 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL E 227 " --> pdb=" O VAL E 117 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU E 228 " --> pdb=" O ILE E 183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 188 through 191 removed outlier: 3.555A pdb=" N ARG E 190 " --> pdb=" O HIS E 182 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU E 228 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL E 227 " --> pdb=" O VAL E 117 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA E 235 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 284 through 286 Processing sheet with id=AB4, first strand: chain 'F' and resid 126 through 127 removed outlier: 3.715A pdb=" N ALA F 126 " --> pdb=" O ALA F 31 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU F 30 " --> pdb=" O PHE F 354 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 37 through 38 removed outlier: 4.197A pdb=" N VAL F 227 " --> pdb=" O VAL F 117 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU F 228 " --> pdb=" O ILE F 183 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE F 180 " --> pdb=" O TRP F 192 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG F 190 " --> pdb=" O HIS F 182 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 37 through 38 Processing sheet with id=AB7, first strand: chain 'F' and resid 63 through 68 removed outlier: 3.516A pdb=" N VAL F 99 " --> pdb=" O ARG F 63 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL F 67 " --> pdb=" O GLN F 95 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA F 100 " --> pdb=" O VAL F 243 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 247 through 248 removed outlier: 4.559A pdb=" N THR F 263 " --> pdb=" O GLU F 248 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 305 through 306 removed outlier: 3.630A pdb=" N LYS F 311 " --> pdb=" O VAL F 306 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 30 through 31 Processing sheet with id=AC2, first strand: chain 'G' and resid 37 through 38 removed outlier: 4.341A pdb=" N VAL G 227 " --> pdb=" O VAL G 117 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU G 228 " --> pdb=" O ILE G 183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 37 through 38 Processing sheet with id=AC4, first strand: chain 'G' and resid 62 through 69 removed outlier: 3.609A pdb=" N ASN G 93 " --> pdb=" O GLY G 69 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N SER G 261 " --> pdb=" O LEU G 94 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N THR G 96 " --> pdb=" O SER G 261 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR G 263 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASP G 98 " --> pdb=" O THR G 263 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR G 263 " --> pdb=" O GLU G 248 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 284 through 286 Processing sheet with id=AC6, first strand: chain 'G' and resid 305 through 306 removed outlier: 3.669A pdb=" N LYS G 311 " --> pdb=" O VAL G 306 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 126 through 127 Processing sheet with id=AC8, first strand: chain 'H' and resid 37 through 38 removed outlier: 4.410A pdb=" N VAL H 227 " --> pdb=" O VAL H 117 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA H 175 " --> pdb=" O ARG H 236 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 37 through 38 Processing sheet with id=AD1, first strand: chain 'H' and resid 62 through 69 removed outlier: 4.591A pdb=" N ALA H 100 " --> pdb=" O VAL H 243 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 247 through 248 removed outlier: 4.725A pdb=" N THR H 263 " --> pdb=" O GLU H 248 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 284 through 286 Processing sheet with id=AD4, first strand: chain 'H' and resid 305 through 306 Processing sheet with id=AD5, first strand: chain 'I' and resid 30 through 31 Processing sheet with id=AD6, first strand: chain 'I' and resid 37 through 38 removed outlier: 4.309A pdb=" N VAL I 227 " --> pdb=" O VAL I 117 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU I 228 " --> pdb=" O ILE I 183 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL I 176 " --> pdb=" O ASP I 195 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASP I 195 " --> pdb=" O VAL I 176 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL I 178 " --> pdb=" O ARG I 193 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ARG I 193 " --> pdb=" O VAL I 178 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE I 180 " --> pdb=" O ALA I 191 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA I 191 " --> pdb=" O ILE I 180 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N HIS I 182 " --> pdb=" O ALA I 189 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 37 through 38 Processing sheet with id=AD8, first strand: chain 'I' and resid 62 through 68 removed outlier: 4.479A pdb=" N ALA I 100 " --> pdb=" O VAL I 243 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 62 through 68 removed outlier: 7.374A pdb=" N SER I 261 " --> pdb=" O LEU I 94 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N THR I 96 " --> pdb=" O SER I 261 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 305 through 306 removed outlier: 3.612A pdb=" N LYS I 311 " --> pdb=" O VAL I 306 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 126 through 127 Processing sheet with id=AE3, first strand: chain 'J' and resid 37 through 38 removed outlier: 4.530A pdb=" N LEU J 228 " --> pdb=" O ILE J 183 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA J 175 " --> pdb=" O ARG J 236 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 188 through 191 removed outlier: 4.122A pdb=" N ARG J 190 " --> pdb=" O HIS J 182 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA J 175 " --> pdb=" O ARG J 236 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU J 228 " --> pdb=" O ILE J 183 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 62 through 69 removed outlier: 4.468A pdb=" N ALA J 100 " --> pdb=" O VAL J 243 " (cutoff:3.500A) 791 hydrogen bonds defined for protein. 2160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 4.96 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 4059 1.25 - 1.39: 6239 1.39 - 1.53: 13844 1.53 - 1.67: 1100 1.67 - 1.81: 50 Bond restraints: 25292 Sorted by residual: bond pdb=" C GLY G 46 " pdb=" O GLY G 46 " ideal model delta sigma weight residual 1.233 1.114 0.119 1.25e-02 6.40e+03 9.01e+01 bond pdb=" C SER G 44 " pdb=" O SER G 44 " ideal model delta sigma weight residual 1.234 1.121 0.113 1.24e-02 6.50e+03 8.26e+01 bond pdb=" CA PRO G 58 " pdb=" C PRO G 58 " ideal model delta sigma weight residual 1.521 1.410 0.111 1.24e-02 6.50e+03 8.02e+01 bond pdb=" C PRO G 58 " pdb=" O PRO G 58 " ideal model delta sigma weight residual 1.233 1.130 0.103 1.19e-02 7.06e+03 7.55e+01 bond pdb=" CA GLN G 50 " pdb=" C GLN G 50 " ideal model delta sigma weight residual 1.524 1.422 0.102 1.26e-02 6.30e+03 6.56e+01 ... (remaining 25287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 33710 3.16 - 6.32: 777 6.32 - 9.48: 74 9.48 - 12.64: 15 12.64 - 15.79: 9 Bond angle restraints: 34585 Sorted by residual: angle pdb=" N ALA G 49 " pdb=" CA ALA G 49 " pdb=" C ALA G 49 " ideal model delta sigma weight residual 110.44 96.11 14.33 1.20e+00 6.94e-01 1.43e+02 angle pdb=" C TRP G 57 " pdb=" CA TRP G 57 " pdb=" CB TRP G 57 " ideal model delta sigma weight residual 109.15 124.94 -15.79 1.60e+00 3.91e-01 9.74e+01 angle pdb=" C TRP G 48 " pdb=" N ALA G 49 " pdb=" CA ALA G 49 " ideal model delta sigma weight residual 123.34 138.67 -15.33 1.80e+00 3.09e-01 7.25e+01 angle pdb=" CA GLU A 18 " pdb=" CB GLU A 18 " pdb=" CG GLU A 18 " ideal model delta sigma weight residual 114.10 129.31 -15.21 2.00e+00 2.50e-01 5.78e+01 angle pdb=" CA GLU B 18 " pdb=" CB GLU B 18 " pdb=" CG GLU B 18 " ideal model delta sigma weight residual 114.10 129.30 -15.20 2.00e+00 2.50e-01 5.77e+01 ... (remaining 34580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.35: 14529 28.35 - 56.69: 471 56.69 - 85.04: 91 85.04 - 113.38: 2 113.38 - 141.73: 1 Dihedral angle restraints: 15094 sinusoidal: 6487 harmonic: 8607 Sorted by residual: dihedral pdb=" C4' C L 29 " pdb=" C3' C L 29 " pdb=" C2' C L 29 " pdb=" C1' C L 29 " ideal model delta sinusoidal sigma weight residual 36.35 -38.98 75.32 1 3.10e+00 1.04e-01 7.46e+02 dihedral pdb=" C4' A L 3 " pdb=" C3' A L 3 " pdb=" C2' A L 3 " pdb=" C1' A L 3 " ideal model delta sinusoidal sigma weight residual 36.34 -38.87 75.22 1 3.10e+00 1.04e-01 7.44e+02 dihedral pdb=" C4' C L 28 " pdb=" C3' C L 28 " pdb=" C2' C L 28 " pdb=" C1' C L 28 " ideal model delta sinusoidal sigma weight residual 36.35 -38.57 74.91 1 3.10e+00 1.04e-01 7.39e+02 ... (remaining 15091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.219: 3783 0.219 - 0.437: 80 0.437 - 0.656: 1 0.656 - 0.874: 0 0.874 - 1.093: 2 Chirality restraints: 3866 Sorted by residual: chirality pdb=" CA SER G 54 " pdb=" N SER G 54 " pdb=" C SER G 54 " pdb=" CB SER G 54 " both_signs ideal model delta sigma weight residual False 2.51 1.42 1.09 2.00e-01 2.50e+01 2.99e+01 chirality pdb=" CA TRP G 57 " pdb=" N TRP G 57 " pdb=" C TRP G 57 " pdb=" CB TRP G 57 " both_signs ideal model delta sigma weight residual False 2.51 1.63 0.88 2.00e-01 2.50e+01 1.92e+01 chirality pdb=" CA ALA G 49 " pdb=" N ALA G 49 " pdb=" C ALA G 49 " pdb=" CB ALA G 49 " both_signs ideal model delta sigma weight residual False 2.48 2.97 -0.48 2.00e-01 2.50e+01 5.77e+00 ... (remaining 3863 not shown) Planarity restraints: 4337 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 47 " -0.024 2.00e-02 2.50e+03 4.49e-02 2.02e+01 pdb=" C ALA G 47 " 0.078 2.00e-02 2.50e+03 pdb=" O ALA G 47 " -0.028 2.00e-02 2.50e+03 pdb=" N TRP G 48 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 329 " -0.029 2.00e-02 2.50e+03 2.39e-02 1.43e+01 pdb=" CG TRP F 329 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP F 329 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP F 329 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 329 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP F 329 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP F 329 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 329 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 329 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 329 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 268 " 0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C ARG E 268 " -0.065 2.00e-02 2.50e+03 pdb=" O ARG E 268 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP E 269 " 0.022 2.00e-02 2.50e+03 ... (remaining 4334 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5206 2.78 - 3.31: 20588 3.31 - 3.84: 40650 3.84 - 4.37: 47886 4.37 - 4.90: 81096 Nonbonded interactions: 195426 Sorted by model distance: nonbonded pdb=" O2' U L 39 " pdb=" OP2 G L 41 " model vdw 2.253 3.040 nonbonded pdb=" OD1 ASP C 107 " pdb=" OG SER C 252 " model vdw 2.268 3.040 nonbonded pdb=" OH TYR E 323 " pdb=" O SER F 72 " model vdw 2.278 3.040 nonbonded pdb=" OD1 ASN A 12 " pdb=" OG SER A 15 " model vdw 2.288 3.040 nonbonded pdb=" OD1 ASN B 12 " pdb=" OG SER B 15 " model vdw 2.289 3.040 ... (remaining 195421 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 'A' selection = chain 'B' } ncs_group { reference = (chain 'E' and resid 24 through 356) selection = (chain 'F' and (resid 24 through 62 or resid 100 through 249 or resid 262 throug \ h 356)) selection = (chain 'G' and (resid 24 through 62 or resid 100 through 249 or resid 262 throug \ h 356)) selection = (chain 'H' and (resid 24 through 62 or resid 100 through 249 or resid 262 throug \ h 356)) selection = (chain 'I' and (resid 24 through 62 or resid 100 through 249 or resid 262 throug \ h 356)) } 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: 7.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.450 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 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 : 0.010 0.137 25292 Z= 0.460 Angle : 1.148 15.794 34585 Z= 0.630 Chirality : 0.074 1.093 3866 Planarity : 0.008 0.080 4337 Dihedral : 13.909 141.726 9530 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.63 % Favored : 91.31 % Rotamer: Outliers : 1.16 % Allowed : 3.39 % Favored : 95.45 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.98 (0.12), residues: 2956 helix: -3.33 (0.13), residues: 719 sheet: -0.46 (0.23), residues: 478 loop : -3.14 (0.11), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.002 ARG G 164 TYR 0.036 0.004 TYR E 156 PHE 0.041 0.004 PHE C 211 TRP 0.065 0.006 TRP F 329 HIS 0.024 0.004 HIS D 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00957 / 0.46 (25292) covalent geometry : angle 1.14844 / 0.63 (34585) hydrogen bonds : bond 0.21426 / 14.02 ( 728) hydrogen bonds : angle 7.95992 / 5.50 ( 2160) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 360 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.4799 (ptm) cc_final: 0.3267 (tmm) REVERT: C 65 LEU cc_start: 0.8939 (tp) cc_final: 0.8734 (tp) REVERT: C 380 ARG cc_start: 0.5999 (tmm160) cc_final: 0.5185 (ttm170) REVERT: C 387 VAL cc_start: 0.5326 (m) cc_final: 0.5000 (p) REVERT: C 395 LEU cc_start: 0.7798 (mm) cc_final: 0.7011 (pp) REVERT: D 166 ASP cc_start: 0.7179 (t70) cc_final: 0.6824 (t0) REVERT: D 173 GLN cc_start: 0.7567 (mp10) cc_final: 0.7202 (mp10) REVERT: D 181 LEU cc_start: 0.5774 (OUTLIER) cc_final: 0.5389 (tm) REVERT: D 218 ARG cc_start: 0.6067 (pmm150) cc_final: 0.5827 (pmt170) REVERT: E 111 VAL cc_start: 0.7363 (t) cc_final: 0.6993 (p) REVERT: E 179 ARG cc_start: 0.5939 (mtt180) cc_final: 0.5705 (mtt180) REVERT: E 224 SER cc_start: 0.6622 (m) cc_final: 0.6144 (t) REVERT: G 289 TYR cc_start: 0.8578 (p90) cc_final: 0.8261 (p90) REVERT: I 154 ARG cc_start: 0.7450 (ttp80) cc_final: 0.7108 (ttt180) REVERT: J 137 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7789 (pt) REVERT: K 68 ARG cc_start: 0.2438 (ttt90) cc_final: 0.1654 (ptt180) outliers start: 28 outliers final: 5 residues processed: 380 average time/residue: 0.7903 time to fit residues: 336.4169 Evaluate side-chains 249 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 242 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 51 ARG Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 57 TRP Chi-restraints excluded: chain J residue 137 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.0040 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 203 HIS C 237 ASN C 250 ASN C 256 ASN C 283 HIS C 289 HIS D 282 ASN D 293 HIS ** D 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 ASN E 158 HIS E 159 ASN E 328 ASN E 340 GLN ** F 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN F 342 HIS G 50 GLN G 101 ASN ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS H 145 ASN I 55 GLN I 95 GLN I 128 ASN I 226 HIS I 280 ASN J 147 GLN J 241 GLN K 29 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.191856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.141778 restraints weight = 33041.792| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.26 r_work: 0.3662 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25292 Z= 0.139 Angle : 0.830 20.910 34585 Z= 0.381 Chirality : 0.061 0.941 3866 Planarity : 0.005 0.061 4337 Dihedral : 11.521 160.638 4017 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.02 % Allowed : 9.88 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.14), residues: 2956 helix: -1.86 (0.17), residues: 721 sheet: 0.31 (0.24), residues: 459 loop : -2.83 (0.12), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 63 TYR 0.016 0.002 TYR I 156 PHE 0.026 0.001 PHE E 204 TRP 0.024 0.002 TRP F 329 HIS 0.006 0.001 HIS J 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (25292) covalent geometry : angle 0.83010 / 0.38 (34585) hydrogen bonds : bond 0.04152 / 2.73 ( 728) hydrogen bonds : angle 5.23348 / 3.56 ( 2160) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 295 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.4617 (ptm) cc_final: 0.4026 (ptp) REVERT: C 251 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7921 (mt) REVERT: C 380 ARG cc_start: 0.6031 (tmm160) cc_final: 0.5327 (ttm170) REVERT: C 387 VAL cc_start: 0.5315 (m) cc_final: 0.5018 (p) REVERT: D 65 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7364 (tmt170) REVERT: D 106 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7007 (tt0) REVERT: D 166 ASP cc_start: 0.7172 (t70) cc_final: 0.6519 (t0) REVERT: D 170 ARG cc_start: 0.7692 (ptt-90) cc_final: 0.7464 (ptt-90) REVERT: D 173 GLN cc_start: 0.7566 (mp10) cc_final: 0.6872 (mp10) REVERT: D 294 ARG cc_start: 0.7436 (mmp-170) cc_final: 0.7235 (mmm160) REVERT: E 37 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6741 (p0) REVERT: E 111 VAL cc_start: 0.7620 (t) cc_final: 0.7390 (p) REVERT: E 179 ARG cc_start: 0.6044 (mtt180) cc_final: 0.5816 (mtt180) REVERT: E 224 SER cc_start: 0.6720 (m) cc_final: 0.6322 (p) REVERT: F 154 ARG cc_start: 0.8184 (tmt170) cc_final: 0.7882 (ttt-90) REVERT: G 51 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7115 (ppt90) REVERT: G 57 TRP cc_start: 0.7877 (OUTLIER) cc_final: 0.7502 (p90) REVERT: G 301 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7823 (tm-30) REVERT: G 317 LYS cc_start: 0.8269 (ptmm) cc_final: 0.8031 (ttmm) REVERT: H 74 ARG cc_start: 0.8475 (ttm-80) cc_final: 0.8138 (mtt-85) REVERT: H 154 ARG cc_start: 0.7494 (mtp-110) cc_final: 0.7081 (ptm-80) REVERT: H 183 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7991 (mt) REVERT: H 187 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6390 (pp20) REVERT: I 317 LYS cc_start: 0.7218 (mmmm) cc_final: 0.6996 (tppt) REVERT: J 33 GLU cc_start: 0.8713 (tt0) cc_final: 0.8294 (mm-30) REVERT: J 50 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7812 (tp40) REVERT: J 116 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7377 (ptm-80) REVERT: K 68 ARG cc_start: 0.2393 (ttt90) cc_final: 0.1646 (ptt180) REVERT: K 130 ARG cc_start: 0.1082 (OUTLIER) cc_final: 0.0358 (ptm-80) outliers start: 49 outliers final: 12 residues processed: 328 average time/residue: 0.7095 time to fit residues: 264.2438 Evaluate side-chains 266 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 243 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 51 ARG Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 57 TRP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 116 ARG Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain K residue 130 ARG Chi-restraints excluded: chain K residue 157 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 26 optimal weight: 20.0000 chunk 225 optimal weight: 0.0060 chunk 95 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 167 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 162 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 overall best weight: 4.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 21 GLN C 203 HIS C 255 ASN D 82 ASN D 133 GLN E 181 ASN E 342 HIS F 159 ASN ** F 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 ASN G 138 GLN G 182 HIS G 280 ASN G 347 ASN ** H 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 342 HIS I 55 GLN I 95 GLN ** J 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 HIS K 154 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.184904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.132306 restraints weight = 32738.102| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.26 r_work: 0.3535 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.126 25292 Z= 0.338 Angle : 0.935 15.535 34585 Z= 0.451 Chirality : 0.064 0.747 3866 Planarity : 0.007 0.072 4337 Dihedral : 12.241 159.228 4016 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.40 % Favored : 90.56 % Rotamer: Outliers : 4.21 % Allowed : 11.65 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.14), residues: 2956 helix: -1.58 (0.17), residues: 726 sheet: 0.24 (0.23), residues: 491 loop : -2.70 (0.13), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 74 TYR 0.022 0.003 TYR E 265 PHE 0.036 0.003 PHE C 211 TRP 0.026 0.003 TRP E 329 HIS 0.018 0.002 HIS D 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00782 / 0.34 (25292) covalent geometry : angle 0.93512 / 0.45 (34585) hydrogen bonds : bond 0.05115 / 3.38 ( 728) hydrogen bonds : angle 5.25155 / 3.59 ( 2160) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 263 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7649 (tm-30) REVERT: A 36 LYS cc_start: 0.7985 (mtmm) cc_final: 0.7730 (ptpt) REVERT: B 1 MET cc_start: 0.4498 (ptm) cc_final: 0.3835 (ptp) REVERT: B 18 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: C 387 VAL cc_start: 0.5699 (OUTLIER) cc_final: 0.5309 (p) REVERT: C 390 ARG cc_start: 0.6760 (mtp180) cc_final: 0.6412 (mtp-110) REVERT: C 422 LEU cc_start: 0.5940 (OUTLIER) cc_final: 0.4961 (tm) REVERT: D 106 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7190 (tt0) REVERT: D 138 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.7637 (mtm180) REVERT: D 166 ASP cc_start: 0.7192 (t70) cc_final: 0.6580 (t0) REVERT: D 170 ARG cc_start: 0.7586 (ptt-90) cc_final: 0.7341 (ptt-90) REVERT: D 189 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.6978 (mmm160) REVERT: D 294 ARG cc_start: 0.7563 (mmp-170) cc_final: 0.7252 (mmm160) REVERT: E 37 ASP cc_start: 0.7339 (OUTLIER) cc_final: 0.6828 (p0) REVERT: E 111 VAL cc_start: 0.7735 (t) cc_final: 0.7511 (p) REVERT: E 145 ASN cc_start: 0.5396 (m-40) cc_final: 0.4928 (m-40) REVERT: E 224 SER cc_start: 0.6672 (m) cc_final: 0.6204 (t) REVERT: F 154 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7873 (ttt-90) REVERT: G 51 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7164 (ppt90) REVERT: G 57 TRP cc_start: 0.7973 (OUTLIER) cc_final: 0.7511 (p-90) REVERT: G 239 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.7958 (m-30) REVERT: G 301 GLU cc_start: 0.8251 (tm-30) cc_final: 0.8035 (tm-30) REVERT: G 317 LYS cc_start: 0.8363 (ptmm) cc_final: 0.8160 (ttmm) REVERT: H 154 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7237 (ptm-80) REVERT: H 177 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8039 (tp30) REVERT: I 259 GLN cc_start: 0.6824 (tp40) cc_final: 0.6365 (tp40) REVERT: I 317 LYS cc_start: 0.7201 (mmmm) cc_final: 0.6938 (tppt) REVERT: J 64 GLU cc_start: 0.8086 (pt0) cc_final: 0.7821 (pt0) REVERT: J 123 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8762 (p) REVERT: J 137 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7862 (tp) REVERT: K 68 ARG cc_start: 0.2517 (ttt90) cc_final: 0.1698 (ptt180) REVERT: K 130 ARG cc_start: 0.0946 (OUTLIER) cc_final: 0.0008 (ptm-80) outliers start: 102 outliers final: 33 residues processed: 329 average time/residue: 0.7252 time to fit residues: 270.2605 Evaluate side-chains 286 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 236 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 189 ARG Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 288 TRP Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 154 ARG Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 51 ARG Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 57 TRP Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 230 GLU Chi-restraints excluded: chain G residue 239 ASP Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 154 ARG Chi-restraints excluded: chain H residue 177 GLU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 130 ARG Chi-restraints excluded: chain K residue 157 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 252 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 251 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 216 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 21 GLN C 203 HIS C 283 HIS ** F 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 GLN I 95 GLN K 3 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.190173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.138577 restraints weight = 32716.942| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.27 r_work: 0.3624 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 25292 Z= 0.134 Angle : 0.697 13.125 34585 Z= 0.337 Chirality : 0.050 0.352 3866 Planarity : 0.005 0.058 4337 Dihedral : 12.039 155.920 4016 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.39 % Allowed : 13.68 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.14), residues: 2956 helix: -0.87 (0.18), residues: 732 sheet: 0.51 (0.24), residues: 496 loop : -2.59 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 63 TYR 0.015 0.001 TYR J 289 PHE 0.032 0.001 PHE E 322 TRP 0.019 0.001 TRP C 394 HIS 0.020 0.001 HIS K 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (25292) covalent geometry : angle 0.69653 / 0.34 (34585) hydrogen bonds : bond 0.03505 / 2.30 ( 728) hydrogen bonds : angle 4.73224 / 3.23 ( 2160) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 245 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.7770 (mtmm) cc_final: 0.7509 (ptpt) REVERT: B 1 MET cc_start: 0.4458 (ptm) cc_final: 0.3781 (ptp) REVERT: C 387 VAL cc_start: 0.5447 (OUTLIER) cc_final: 0.5097 (p) REVERT: C 390 ARG cc_start: 0.6764 (mtp180) cc_final: 0.6413 (mtp-110) REVERT: C 420 LYS cc_start: 0.8153 (ptmt) cc_final: 0.7728 (pptt) REVERT: C 422 LEU cc_start: 0.5773 (OUTLIER) cc_final: 0.5042 (tm) REVERT: C 426 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7338 (tppt) REVERT: D 50 ILE cc_start: 0.7136 (OUTLIER) cc_final: 0.6788 (mp) REVERT: D 106 GLU cc_start: 0.7379 (tp30) cc_final: 0.7096 (tt0) REVERT: D 166 ASP cc_start: 0.7128 (t70) cc_final: 0.6544 (t0) REVERT: D 170 ARG cc_start: 0.7631 (ptt-90) cc_final: 0.7430 (ptt-90) REVERT: D 181 LEU cc_start: 0.5937 (OUTLIER) cc_final: 0.5415 (tm) REVERT: D 294 ARG cc_start: 0.7524 (mmp-170) cc_final: 0.7177 (mmm160) REVERT: E 179 ARG cc_start: 0.6289 (OUTLIER) cc_final: 0.5982 (mtt180) REVERT: E 224 SER cc_start: 0.6737 (m) cc_final: 0.6320 (p) REVERT: F 68 ARG cc_start: 0.6996 (ttp-170) cc_final: 0.6733 (ttp-170) REVERT: F 154 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7885 (ttt-90) REVERT: G 44 SER cc_start: 0.8799 (OUTLIER) cc_final: 0.8507 (p) REVERT: G 51 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7101 (ppt90) REVERT: G 57 TRP cc_start: 0.7808 (OUTLIER) cc_final: 0.6993 (p90) REVERT: G 301 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7807 (tm-30) REVERT: H 154 ARG cc_start: 0.7545 (mtp-110) cc_final: 0.7156 (ptm-80) REVERT: H 183 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7979 (mt) REVERT: I 99 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8599 (p) REVERT: I 146 ASP cc_start: 0.7639 (t70) cc_final: 0.7184 (t70) REVERT: I 259 GLN cc_start: 0.6727 (tp40) cc_final: 0.6327 (tp40) REVERT: I 317 LYS cc_start: 0.7212 (mmmm) cc_final: 0.6966 (tppt) REVERT: J 116 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.8081 (ptt-90) REVERT: J 137 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7835 (tp) REVERT: J 242 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8537 (tp30) REVERT: K 8 ARG cc_start: 0.2202 (ptp90) cc_final: 0.1884 (mtm110) REVERT: K 54 LEU cc_start: 0.1102 (tm) cc_final: 0.0402 (pp) REVERT: K 68 ARG cc_start: 0.2547 (ttt90) cc_final: 0.1691 (ptt180) REVERT: K 130 ARG cc_start: 0.1068 (OUTLIER) cc_final: 0.0110 (ptm-80) outliers start: 82 outliers final: 29 residues processed: 297 average time/residue: 0.6887 time to fit residues: 231.7783 Evaluate side-chains 276 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 231 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 247 GLN Chi-restraints excluded: chain F residue 154 ARG Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 51 ARG Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 57 TRP Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 356 GLU Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain J residue 116 ARG Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 130 ARG Chi-restraints excluded: chain K residue 157 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 236 optimal weight: 5.9990 chunk 251 optimal weight: 6.9990 chunk 110 optimal weight: 0.0470 chunk 248 optimal weight: 7.9990 chunk 296 optimal weight: 20.0000 chunk 127 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 160 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 102 optimal weight: 4.9990 overall best weight: 4.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 GLN C 203 HIS C 413 GLN ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 HIS ** F 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 GLN G 159 ASN G 347 ASN ** H 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 95 GLN ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.184565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.132811 restraints weight = 32617.928| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.23 r_work: 0.3538 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.142 25292 Z= 0.308 Angle : 0.858 13.280 34585 Z= 0.415 Chirality : 0.060 0.553 3866 Planarity : 0.006 0.065 4337 Dihedral : 12.365 160.220 4016 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 4.67 % Allowed : 13.84 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.15), residues: 2956 helix: -1.04 (0.18), residues: 731 sheet: 0.43 (0.23), residues: 504 loop : -2.57 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 63 TYR 0.018 0.002 TYR F 303 PHE 0.035 0.002 PHE C 211 TRP 0.022 0.002 TRP C 228 HIS 0.015 0.002 HIS K 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00709 / 0.31 (25292) covalent geometry : angle 0.85794 / 0.42 (34585) hydrogen bonds : bond 0.04608 / 3.03 ( 728) hydrogen bonds : angle 4.99370 / 3.41 ( 2160) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 245 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7586 (tm-30) REVERT: B 1 MET cc_start: 0.4433 (ptm) cc_final: 0.4046 (ptp) REVERT: B 18 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: C 387 VAL cc_start: 0.5649 (OUTLIER) cc_final: 0.5221 (p) REVERT: C 390 ARG cc_start: 0.6706 (mtp180) cc_final: 0.6336 (mtp-110) REVERT: C 420 LYS cc_start: 0.8136 (ptmt) cc_final: 0.7726 (pptt) REVERT: C 422 LEU cc_start: 0.5850 (OUTLIER) cc_final: 0.5038 (tm) REVERT: C 426 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7393 (tppt) REVERT: D 50 ILE cc_start: 0.7245 (OUTLIER) cc_final: 0.6946 (mp) REVERT: D 106 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7214 (tt0) REVERT: D 166 ASP cc_start: 0.7126 (t70) cc_final: 0.6549 (t0) REVERT: D 170 ARG cc_start: 0.7578 (ptt-90) cc_final: 0.7320 (ptt-90) REVERT: D 189 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.6871 (mmm160) REVERT: D 294 ARG cc_start: 0.7581 (mmp-170) cc_final: 0.7238 (mmm160) REVERT: E 37 ASP cc_start: 0.7320 (OUTLIER) cc_final: 0.6776 (p0) REVERT: E 133 ARG cc_start: 0.6461 (tpt-90) cc_final: 0.6146 (ttt180) REVERT: E 179 ARG cc_start: 0.6275 (OUTLIER) cc_final: 0.6023 (mtt180) REVERT: E 224 SER cc_start: 0.6684 (m) cc_final: 0.6194 (p) REVERT: E 289 TYR cc_start: 0.3892 (p90) cc_final: 0.3629 (p90) REVERT: E 301 GLU cc_start: 0.6893 (tm-30) cc_final: 0.6602 (tm-30) REVERT: F 154 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7949 (ttt-90) REVERT: G 51 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7082 (ppt90) REVERT: G 57 TRP cc_start: 0.7976 (OUTLIER) cc_final: 0.7615 (p90) REVERT: G 301 GLU cc_start: 0.8274 (tm-30) cc_final: 0.8053 (tm-30) REVERT: H 154 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7260 (ptm-80) REVERT: H 177 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8009 (tp30) REVERT: H 317 LYS cc_start: 0.7692 (mmmm) cc_final: 0.7281 (tmmt) REVERT: I 99 VAL cc_start: 0.8902 (OUTLIER) cc_final: 0.8678 (p) REVERT: I 259 GLN cc_start: 0.6698 (tp40) cc_final: 0.6297 (tp40) REVERT: I 317 LYS cc_start: 0.7268 (mmmm) cc_final: 0.6985 (tppt) REVERT: J 64 GLU cc_start: 0.8084 (pt0) cc_final: 0.7827 (pt0) REVERT: J 137 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7949 (tp) REVERT: J 242 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8595 (tt0) REVERT: J 319 LYS cc_start: 0.6628 (tmtm) cc_final: 0.6394 (tptm) REVERT: K 54 LEU cc_start: 0.1123 (tm) cc_final: 0.0444 (pp) REVERT: K 68 ARG cc_start: 0.2683 (ttt90) cc_final: 0.1800 (ptt180) REVERT: K 130 ARG cc_start: 0.1112 (OUTLIER) cc_final: 0.0196 (ptm-80) outliers start: 113 outliers final: 50 residues processed: 319 average time/residue: 0.6759 time to fit residues: 244.9080 Evaluate side-chains 305 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 236 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 272 TRP Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 189 ARG Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 288 TRP Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 154 ARG Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 51 ARG Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 57 TRP Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 95 GLN Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 154 ARG Chi-restraints excluded: chain H residue 177 GLU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 215 GLU Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 130 ARG Chi-restraints excluded: chain K residue 157 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 131 optimal weight: 0.9980 chunk 203 optimal weight: 0.9990 chunk 280 optimal weight: 20.0000 chunk 281 optimal weight: 30.0000 chunk 221 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 chunk 34 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 11 GLN B 21 GLN C 203 HIS C 250 ASN E 247 GLN F 101 ASN F 259 GLN G 138 GLN ** H 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 95 GLN K 3 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.190127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.139237 restraints weight = 32512.707| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.24 r_work: 0.3621 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25292 Z= 0.120 Angle : 0.673 13.089 34585 Z= 0.325 Chirality : 0.049 0.351 3866 Planarity : 0.004 0.060 4337 Dihedral : 12.054 158.821 4016 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.84 % Allowed : 15.29 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.15), residues: 2956 helix: -0.40 (0.19), residues: 731 sheet: 0.65 (0.24), residues: 494 loop : -2.43 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 63 TYR 0.015 0.001 TYR H 289 PHE 0.027 0.001 PHE C 211 TRP 0.023 0.001 TRP C 394 HIS 0.015 0.001 HIS K 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (25292) covalent geometry : angle 0.67295 / 0.33 (34585) hydrogen bonds : bond 0.03257 / 2.12 ( 728) hydrogen bonds : angle 4.56801 / 3.10 ( 2160) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 249 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8609 (tt0) REVERT: B 1 MET cc_start: 0.4399 (ptm) cc_final: 0.3959 (ptp) REVERT: B 38 GLN cc_start: 0.8279 (tt0) cc_final: 0.7795 (tm-30) REVERT: C 49 ARG cc_start: 0.2820 (tpm170) cc_final: 0.2325 (tpm170) REVERT: C 387 VAL cc_start: 0.5505 (OUTLIER) cc_final: 0.5129 (p) REVERT: C 390 ARG cc_start: 0.6760 (mtp180) cc_final: 0.6450 (mtp-110) REVERT: C 420 LYS cc_start: 0.8099 (ptmt) cc_final: 0.7651 (pptt) REVERT: C 422 LEU cc_start: 0.5762 (OUTLIER) cc_final: 0.5002 (tm) REVERT: C 426 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7403 (tppt) REVERT: D 106 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7138 (tt0) REVERT: D 166 ASP cc_start: 0.7042 (t70) cc_final: 0.6474 (t0) REVERT: D 170 ARG cc_start: 0.7540 (ptt-90) cc_final: 0.7311 (ptt-90) REVERT: D 181 LEU cc_start: 0.5903 (OUTLIER) cc_final: 0.5619 (tp) REVERT: D 294 ARG cc_start: 0.7501 (mmp-170) cc_final: 0.7134 (mmm160) REVERT: E 179 ARG cc_start: 0.6246 (OUTLIER) cc_final: 0.5988 (mtt180) REVERT: E 224 SER cc_start: 0.6736 (m) cc_final: 0.6313 (p) REVERT: E 289 TYR cc_start: 0.3503 (p90) cc_final: 0.3079 (p90) REVERT: E 301 GLU cc_start: 0.7005 (tm-30) cc_final: 0.6562 (tm-30) REVERT: F 154 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7853 (ttt-90) REVERT: G 44 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8529 (p) REVERT: G 51 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7110 (ppt90) REVERT: G 95 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8017 (pm20) REVERT: G 301 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7867 (tm-30) REVERT: H 154 ARG cc_start: 0.7534 (mtp-110) cc_final: 0.7111 (ptm-80) REVERT: H 183 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7998 (mt) REVERT: H 317 LYS cc_start: 0.7547 (mmmm) cc_final: 0.7183 (tmmt) REVERT: I 71 ILE cc_start: 0.7936 (mm) cc_final: 0.7419 (tp) REVERT: I 259 GLN cc_start: 0.6633 (tp40) cc_final: 0.6246 (tp40) REVERT: I 317 LYS cc_start: 0.7248 (mmmm) cc_final: 0.6968 (tppt) REVERT: J 50 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7737 (tp40) REVERT: J 94 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8222 (mt) REVERT: J 116 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.8070 (ptt-90) REVERT: J 137 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7927 (tp) REVERT: J 242 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8495 (tp30) REVERT: K 8 ARG cc_start: 0.1886 (ptp90) cc_final: 0.1648 (mtm110) REVERT: K 54 LEU cc_start: 0.1077 (tm) cc_final: 0.0410 (pp) REVERT: K 68 ARG cc_start: 0.2533 (ttt90) cc_final: 0.1759 (ptt180) REVERT: K 122 LEU cc_start: 0.0339 (OUTLIER) cc_final: -0.0242 (mm) REVERT: K 130 ARG cc_start: 0.1158 (OUTLIER) cc_final: 0.0249 (ptm-80) outliers start: 93 outliers final: 34 residues processed: 314 average time/residue: 0.7044 time to fit residues: 250.3497 Evaluate side-chains 273 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 220 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 272 TRP Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 154 ARG Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 51 ARG Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 95 GLN Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 215 GLU Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 303 TYR Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 116 ARG Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 130 ARG Chi-restraints excluded: chain K residue 157 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 99 optimal weight: 2.9990 chunk 267 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 133 optimal weight: 8.9990 chunk 264 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 250 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 61 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 53.8763 > 50:) chunk 134 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 21 GLN C 250 ASN G 138 GLN G 347 ASN ** H 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 95 GLN K 3 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.189097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.137911 restraints weight = 32580.077| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.25 r_work: 0.3604 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25292 Z= 0.149 Angle : 0.686 12.508 34585 Z= 0.331 Chirality : 0.050 0.357 3866 Planarity : 0.004 0.059 4337 Dihedral : 11.916 160.011 4011 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 4.01 % Allowed : 15.58 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.15), residues: 2956 helix: -0.26 (0.19), residues: 731 sheet: 0.69 (0.24), residues: 484 loop : -2.34 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 332 TYR 0.014 0.001 TYR J 313 PHE 0.028 0.001 PHE C 211 TRP 0.024 0.001 TRP C 394 HIS 0.005 0.001 HIS J 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (25292) covalent geometry : angle 0.68561 / 0.33 (34585) hydrogen bonds : bond 0.03383 / 2.21 ( 728) hydrogen bonds : angle 4.50364 / 3.06 ( 2160) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 234 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.6141 (tttm) cc_final: 0.5913 (tttm) REVERT: A 18 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7596 (tm-30) REVERT: A 21 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8532 (tt0) REVERT: A 23 GLU cc_start: 0.7632 (tp30) cc_final: 0.7342 (tp30) REVERT: B 1 MET cc_start: 0.4394 (ptm) cc_final: 0.3938 (ptp) REVERT: B 38 GLN cc_start: 0.8255 (tt0) cc_final: 0.7669 (tm-30) REVERT: C 49 ARG cc_start: 0.2849 (tpm170) cc_final: 0.2382 (tpm170) REVERT: C 390 ARG cc_start: 0.6718 (mtp180) cc_final: 0.6404 (mtp-110) REVERT: C 420 LYS cc_start: 0.8106 (ptmt) cc_final: 0.7663 (pptt) REVERT: C 422 LEU cc_start: 0.5759 (OUTLIER) cc_final: 0.4984 (tm) REVERT: C 426 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7361 (tppt) REVERT: D 50 ILE cc_start: 0.7130 (OUTLIER) cc_final: 0.6773 (mp) REVERT: D 106 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7188 (tt0) REVERT: D 166 ASP cc_start: 0.7044 (t70) cc_final: 0.6479 (t0) REVERT: D 170 ARG cc_start: 0.7544 (ptt-90) cc_final: 0.7282 (ptt-90) REVERT: D 181 LEU cc_start: 0.5951 (OUTLIER) cc_final: 0.5449 (tm) REVERT: D 294 ARG cc_start: 0.7495 (mmp-170) cc_final: 0.7121 (mmm160) REVERT: E 179 ARG cc_start: 0.6232 (OUTLIER) cc_final: 0.5956 (mtt180) REVERT: E 224 SER cc_start: 0.6770 (m) cc_final: 0.6342 (p) REVERT: E 289 TYR cc_start: 0.3524 (p90) cc_final: 0.3222 (p90) REVERT: E 301 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6622 (tm-30) REVERT: F 154 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7876 (ttt-90) REVERT: F 242 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7973 (tt0) REVERT: G 44 SER cc_start: 0.8849 (OUTLIER) cc_final: 0.8531 (p) REVERT: G 51 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7138 (ppt90) REVERT: G 95 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7981 (pm20) REVERT: G 301 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7858 (tm-30) REVERT: G 334 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7197 (mt-10) REVERT: H 154 ARG cc_start: 0.7553 (mtp-110) cc_final: 0.7165 (ptm-80) REVERT: H 187 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6793 (pp20) REVERT: H 317 LYS cc_start: 0.7485 (mmmm) cc_final: 0.7135 (tmmt) REVERT: I 71 ILE cc_start: 0.8005 (mm) cc_final: 0.7483 (tp) REVERT: I 99 VAL cc_start: 0.8857 (OUTLIER) cc_final: 0.8615 (p) REVERT: I 259 GLN cc_start: 0.6641 (tp40) cc_final: 0.6242 (tp40) REVERT: I 317 LYS cc_start: 0.7212 (mmmm) cc_final: 0.6926 (tppt) REVERT: J 116 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.8054 (ptt-90) REVERT: J 137 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7992 (tp) REVERT: J 242 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8503 (tp30) REVERT: J 259 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.7155 (tt0) REVERT: K 8 ARG cc_start: 0.1934 (ptp90) cc_final: 0.1682 (mtm110) REVERT: K 54 LEU cc_start: 0.1101 (tm) cc_final: 0.0430 (pp) REVERT: K 68 ARG cc_start: 0.2610 (ttt90) cc_final: 0.1808 (ptt180) REVERT: K 122 LEU cc_start: 0.0277 (OUTLIER) cc_final: -0.0277 (mm) REVERT: K 130 ARG cc_start: 0.1124 (OUTLIER) cc_final: 0.0225 (ptm-80) outliers start: 97 outliers final: 46 residues processed: 303 average time/residue: 0.6849 time to fit residues: 235.6793 Evaluate side-chains 288 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 220 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 272 TRP Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 154 ARG Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 51 ARG Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 95 GLN Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 215 GLU Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 303 TYR Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 116 ARG Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain J residue 259 GLN Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 130 ARG Chi-restraints excluded: chain K residue 157 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 50 optimal weight: 30.0000 chunk 67 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 62 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 178 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 21 GLN C 250 ASN G 138 GLN ** H 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 95 GLN K 3 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.189620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.138563 restraints weight = 32500.202| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.23 r_work: 0.3612 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25292 Z= 0.141 Angle : 0.677 12.342 34585 Z= 0.326 Chirality : 0.049 0.354 3866 Planarity : 0.004 0.059 4337 Dihedral : 11.845 159.872 4011 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.51 % Allowed : 16.49 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.15), residues: 2956 helix: -0.10 (0.19), residues: 733 sheet: 0.71 (0.24), residues: 482 loop : -2.29 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 332 TYR 0.015 0.001 TYR J 313 PHE 0.028 0.001 PHE C 211 TRP 0.028 0.001 TRP C 394 HIS 0.013 0.001 HIS K 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (25292) covalent geometry : angle 0.67707 / 0.33 (34585) hydrogen bonds : bond 0.03293 / 2.16 ( 728) hydrogen bonds : angle 4.45426 / 3.03 ( 2160) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 231 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.6179 (tttm) cc_final: 0.5969 (tttm) REVERT: A 23 GLU cc_start: 0.7601 (tp30) cc_final: 0.7344 (tp30) REVERT: B 38 GLN cc_start: 0.8202 (tt0) cc_final: 0.7595 (tm-30) REVERT: C 49 ARG cc_start: 0.3108 (tpm170) cc_final: 0.2686 (tpm170) REVERT: C 390 ARG cc_start: 0.6733 (mtp180) cc_final: 0.6385 (mtp-110) REVERT: C 420 LYS cc_start: 0.8088 (ptmt) cc_final: 0.7666 (pptt) REVERT: C 422 LEU cc_start: 0.5667 (OUTLIER) cc_final: 0.4888 (tm) REVERT: C 426 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7414 (tppt) REVERT: D 50 ILE cc_start: 0.7107 (OUTLIER) cc_final: 0.6736 (mp) REVERT: D 90 ARG cc_start: 0.7270 (pmm-80) cc_final: 0.6452 (ttp80) REVERT: D 106 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7162 (tt0) REVERT: D 166 ASP cc_start: 0.7095 (t70) cc_final: 0.6536 (t0) REVERT: D 170 ARG cc_start: 0.7529 (ptt-90) cc_final: 0.7274 (ptt-90) REVERT: D 181 LEU cc_start: 0.5890 (OUTLIER) cc_final: 0.5367 (tm) REVERT: D 294 ARG cc_start: 0.7521 (mmp-170) cc_final: 0.7128 (mmm160) REVERT: E 224 SER cc_start: 0.6775 (m) cc_final: 0.6350 (p) REVERT: E 289 TYR cc_start: 0.3527 (p90) cc_final: 0.3075 (p90) REVERT: E 301 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6626 (tm-30) REVERT: F 154 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7855 (ttt-90) REVERT: F 242 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7952 (tt0) REVERT: G 44 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8528 (p) REVERT: G 51 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7148 (ppt90) REVERT: G 95 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7983 (pm20) REVERT: G 230 GLU cc_start: 0.7924 (tt0) cc_final: 0.7578 (tp30) REVERT: G 301 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7833 (tm-30) REVERT: G 334 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7191 (mt-10) REVERT: H 154 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7164 (ptm-80) REVERT: H 183 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8017 (mt) REVERT: H 187 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6539 (pp20) REVERT: H 317 LYS cc_start: 0.7433 (mmmm) cc_final: 0.7106 (tmmt) REVERT: I 71 ILE cc_start: 0.8030 (mm) cc_final: 0.7490 (tp) REVERT: I 99 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8618 (p) REVERT: I 259 GLN cc_start: 0.6663 (tp40) cc_final: 0.6327 (tp40) REVERT: I 317 LYS cc_start: 0.7238 (mmmm) cc_final: 0.6979 (tppt) REVERT: J 50 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7738 (tp40) REVERT: J 116 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.8049 (ptt-90) REVERT: J 242 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8491 (tp30) REVERT: K 8 ARG cc_start: 0.1944 (ptp90) cc_final: 0.1571 (mtm110) REVERT: K 54 LEU cc_start: 0.1193 (tm) cc_final: 0.0516 (pp) REVERT: K 68 ARG cc_start: 0.2592 (ttt90) cc_final: 0.1832 (ptt180) REVERT: K 122 LEU cc_start: 0.0240 (OUTLIER) cc_final: -0.0294 (mm) REVERT: K 130 ARG cc_start: 0.1118 (OUTLIER) cc_final: 0.0245 (ptm-80) outliers start: 85 outliers final: 43 residues processed: 291 average time/residue: 0.6763 time to fit residues: 223.6584 Evaluate side-chains 281 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 218 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 272 TRP Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 154 ARG Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 51 ARG Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 95 GLN Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 154 ARG Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 303 TYR Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 116 ARG Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 130 ARG Chi-restraints excluded: chain K residue 157 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 25 optimal weight: 0.0470 chunk 80 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 chunk 217 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 21 GLN ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS G 138 GLN ** H 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 95 GLN K 3 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.191211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.140460 restraints weight = 32722.721| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.25 r_work: 0.3635 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25292 Z= 0.117 Angle : 0.652 13.171 34585 Z= 0.313 Chirality : 0.048 0.344 3866 Planarity : 0.004 0.058 4337 Dihedral : 11.711 159.167 4009 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 3.06 % Allowed : 17.15 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.15), residues: 2956 helix: 0.07 (0.19), residues: 736 sheet: 0.72 (0.24), residues: 483 loop : -2.24 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 332 TYR 0.012 0.001 TYR J 303 PHE 0.028 0.001 PHE K 15 TRP 0.033 0.001 TRP C 394 HIS 0.009 0.001 HIS K 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (25292) covalent geometry : angle 0.65159 / 0.31 (34585) hydrogen bonds : bond 0.03056 / 2.00 ( 728) hydrogen bonds : angle 4.34980 / 2.95 ( 2160) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 232 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7583 (tp30) cc_final: 0.7318 (tp30) REVERT: B 38 GLN cc_start: 0.8153 (tt0) cc_final: 0.7580 (tm-30) REVERT: C 49 ARG cc_start: 0.3178 (tpm170) cc_final: 0.2773 (tpm170) REVERT: C 390 ARG cc_start: 0.6723 (mtp180) cc_final: 0.6398 (mtp-110) REVERT: C 420 LYS cc_start: 0.8074 (ptmt) cc_final: 0.7664 (pptt) REVERT: C 422 LEU cc_start: 0.5649 (OUTLIER) cc_final: 0.4874 (tm) REVERT: C 426 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7405 (tppt) REVERT: D 50 ILE cc_start: 0.7102 (OUTLIER) cc_final: 0.6683 (mp) REVERT: D 90 ARG cc_start: 0.7270 (pmm-80) cc_final: 0.6456 (ttp80) REVERT: D 106 GLU cc_start: 0.7386 (tp30) cc_final: 0.7148 (tt0) REVERT: D 166 ASP cc_start: 0.7049 (t70) cc_final: 0.6484 (t0) REVERT: D 170 ARG cc_start: 0.7513 (ptt-90) cc_final: 0.7186 (ptt-90) REVERT: D 181 LEU cc_start: 0.5853 (OUTLIER) cc_final: 0.5338 (tm) REVERT: D 294 ARG cc_start: 0.7522 (mmp-170) cc_final: 0.7128 (mmm160) REVERT: E 145 ASN cc_start: 0.5436 (m-40) cc_final: 0.4760 (m110) REVERT: E 224 SER cc_start: 0.6813 (m) cc_final: 0.6424 (p) REVERT: E 289 TYR cc_start: 0.3428 (p90) cc_final: 0.3127 (p90) REVERT: E 301 GLU cc_start: 0.7053 (tm-30) cc_final: 0.6609 (tm-30) REVERT: F 68 ARG cc_start: 0.6863 (ttp-170) cc_final: 0.6322 (ttp-110) REVERT: F 89 ILE cc_start: 0.4612 (OUTLIER) cc_final: 0.4393 (tp) REVERT: F 154 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7883 (ttt-90) REVERT: F 242 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7988 (tt0) REVERT: G 44 SER cc_start: 0.8790 (OUTLIER) cc_final: 0.8557 (p) REVERT: G 51 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7115 (ppt90) REVERT: G 95 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8128 (pm20) REVERT: G 230 GLU cc_start: 0.7921 (tt0) cc_final: 0.7538 (tp30) REVERT: G 334 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7037 (mt-10) REVERT: H 154 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7137 (ptm-80) REVERT: H 183 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.7959 (mt) REVERT: H 187 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6395 (pp20) REVERT: H 317 LYS cc_start: 0.7393 (mmmm) cc_final: 0.7080 (tmmt) REVERT: I 71 ILE cc_start: 0.8018 (mm) cc_final: 0.7491 (tp) REVERT: I 99 VAL cc_start: 0.8837 (OUTLIER) cc_final: 0.8594 (p) REVERT: I 259 GLN cc_start: 0.6654 (tp40) cc_final: 0.6285 (tp40) REVERT: I 317 LYS cc_start: 0.7248 (mmmm) cc_final: 0.6985 (tppt) REVERT: J 50 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7722 (tp40) REVERT: J 116 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.8029 (ptt-90) REVERT: J 242 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8465 (tp30) REVERT: K 8 ARG cc_start: 0.1902 (ptp90) cc_final: 0.1568 (mtm110) REVERT: K 54 LEU cc_start: 0.1189 (tm) cc_final: 0.0534 (pp) REVERT: K 68 ARG cc_start: 0.2593 (ttt90) cc_final: 0.1818 (ptt180) REVERT: K 122 LEU cc_start: 0.0245 (OUTLIER) cc_final: -0.0274 (mm) REVERT: K 130 ARG cc_start: 0.1156 (OUTLIER) cc_final: 0.0282 (ptm-80) outliers start: 74 outliers final: 40 residues processed: 286 average time/residue: 0.6448 time to fit residues: 210.8317 Evaluate side-chains 282 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 222 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 272 TRP Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 154 ARG Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 51 ARG Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 95 GLN Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 154 ARG Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain H residue 288 TRP Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 303 TYR Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 116 ARG Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 130 ARG Chi-restraints excluded: chain K residue 157 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 268 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 chunk 279 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 176 optimal weight: 10.0000 chunk 11 optimal weight: 0.1980 chunk 33 optimal weight: 6.9990 chunk 196 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 21 GLN ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS G 138 GLN G 347 ASN ** H 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.191494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.140828 restraints weight = 32638.212| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.25 r_work: 0.3649 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25292 Z= 0.114 Angle : 0.648 14.359 34585 Z= 0.310 Chirality : 0.048 0.340 3866 Planarity : 0.004 0.058 4337 Dihedral : 11.633 158.714 4009 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.73 % Allowed : 17.69 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.15), residues: 2956 helix: 0.21 (0.20), residues: 737 sheet: 0.75 (0.24), residues: 485 loop : -2.18 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 63 TYR 0.013 0.001 TYR I 303 PHE 0.025 0.001 PHE C 211 TRP 0.036 0.001 TRP C 394 HIS 0.004 0.001 HIS D 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (25292) covalent geometry : angle 0.64798 / 0.31 (34585) hydrogen bonds : bond 0.02975 / 1.95 ( 728) hydrogen bonds : angle 4.28342 / 2.90 ( 2160) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 231 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: A 2 LYS cc_start: 0.6137 (tttm) cc_final: 0.5827 (tptp) REVERT: A 13 ILE cc_start: 0.8945 (mm) cc_final: 0.8706 (mm) REVERT: B 38 GLN cc_start: 0.8216 (tt0) cc_final: 0.7600 (tm-30) REVERT: B 57 TYR cc_start: 0.8550 (p90) cc_final: 0.8184 (p90) REVERT: C 49 ARG cc_start: 0.3261 (tpm170) cc_final: 0.2857 (tpm170) REVERT: C 390 ARG cc_start: 0.6722 (mtp180) cc_final: 0.6423 (mtp-110) REVERT: C 420 LYS cc_start: 0.8107 (ptmt) cc_final: 0.7695 (pptt) REVERT: C 426 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7132 (tppt) REVERT: D 50 ILE cc_start: 0.7094 (OUTLIER) cc_final: 0.6656 (mp) REVERT: D 106 GLU cc_start: 0.7393 (tp30) cc_final: 0.7136 (tt0) REVERT: D 166 ASP cc_start: 0.7054 (t70) cc_final: 0.6523 (t0) REVERT: D 181 LEU cc_start: 0.5892 (OUTLIER) cc_final: 0.5376 (tm) REVERT: D 294 ARG cc_start: 0.7485 (mmp-170) cc_final: 0.7088 (mmm160) REVERT: E 145 ASN cc_start: 0.5422 (m-40) cc_final: 0.4732 (m110) REVERT: E 224 SER cc_start: 0.6870 (m) cc_final: 0.6477 (p) REVERT: E 289 TYR cc_start: 0.3349 (p90) cc_final: 0.3051 (p90) REVERT: E 301 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6567 (tm-30) REVERT: E 322 PHE cc_start: 0.6728 (t80) cc_final: 0.6527 (t80) REVERT: F 68 ARG cc_start: 0.6857 (ttp-170) cc_final: 0.6365 (ttp-170) REVERT: F 89 ILE cc_start: 0.4550 (OUTLIER) cc_final: 0.4293 (tp) REVERT: F 154 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7836 (ttt-90) REVERT: F 242 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7980 (tt0) REVERT: F 266 SER cc_start: 0.9003 (p) cc_final: 0.8781 (p) REVERT: G 51 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7114 (ppt90) REVERT: G 95 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8049 (pm20) REVERT: G 230 GLU cc_start: 0.7900 (tt0) cc_final: 0.7524 (tp30) REVERT: H 154 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7122 (ptm-80) REVERT: H 183 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.7930 (mt) REVERT: H 187 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6326 (pp20) REVERT: H 317 LYS cc_start: 0.7328 (mmmm) cc_final: 0.7038 (tmmt) REVERT: I 71 ILE cc_start: 0.8011 (mm) cc_final: 0.7485 (tp) REVERT: I 99 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8572 (p) REVERT: I 259 GLN cc_start: 0.6648 (tp40) cc_final: 0.6271 (tp40) REVERT: I 317 LYS cc_start: 0.7237 (mmmm) cc_final: 0.6974 (tppt) REVERT: J 50 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7724 (tp40) REVERT: J 116 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.8006 (ptt-90) REVERT: K 8 ARG cc_start: 0.1943 (ptp90) cc_final: 0.1576 (mtm110) REVERT: K 54 LEU cc_start: 0.1178 (tm) cc_final: 0.0511 (pp) REVERT: K 68 ARG cc_start: 0.2668 (ttt90) cc_final: 0.1864 (ptt180) REVERT: K 122 LEU cc_start: 0.0276 (OUTLIER) cc_final: -0.0228 (mm) REVERT: K 130 ARG cc_start: 0.1167 (OUTLIER) cc_final: 0.0288 (ptm-80) outliers start: 66 outliers final: 38 residues processed: 281 average time/residue: 0.6638 time to fit residues: 212.6715 Evaluate side-chains 274 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 220 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 272 TRP Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 154 ARG Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain G residue 51 ARG Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 95 GLN Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 154 ARG Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 303 TYR Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 116 ARG Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 130 ARG Chi-restraints excluded: chain K residue 157 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 45 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 250 optimal weight: 7.9990 chunk 238 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 223 optimal weight: 0.7980 chunk 267 optimal weight: 0.4980 chunk 170 optimal weight: 0.2980 chunk 180 optimal weight: 7.9990 chunk 216 optimal weight: 4.9990 chunk 277 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 21 GLN ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 GLN ** H 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.193214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.142869 restraints weight = 32790.399| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.26 r_work: 0.3667 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 25292 Z= 0.103 Angle : 0.634 14.933 34585 Z= 0.303 Chirality : 0.047 0.330 3866 Planarity : 0.004 0.057 4337 Dihedral : 11.563 157.878 4009 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.11 % Allowed : 18.43 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.15), residues: 2956 helix: 0.35 (0.20), residues: 738 sheet: 0.73 (0.24), residues: 500 loop : -2.13 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 332 TYR 0.016 0.001 TYR I 303 PHE 0.027 0.001 PHE K 15 TRP 0.037 0.001 TRP C 394 HIS 0.004 0.001 HIS D 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (25292) covalent geometry : angle 0.63422 / 0.30 (34585) hydrogen bonds : bond 0.02808 / 1.84 ( 728) hydrogen bonds : angle 4.19050 / 2.84 ( 2160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12561.22 seconds wall clock time: 213 minutes 33.06 seconds (12813.06 seconds total)