Starting phenix.real_space_refine on Fri Aug 7 14:24:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fs7_29416/08_2026/8fs7_29416.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fs7_29416/08_2026/8fs7_29416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8fs7_29416/08_2026/8fs7_29416.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fs7_29416/08_2026/8fs7_29416.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fs7_29416/08_2026/8fs7_29416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fs7_29416/08_2026/8fs7_29416.map" model { file = "/net/cci-nas-00/data/ceres_data/8fs7_29416/08_2026/8fs7_29416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fs7_29416/08_2026/8fs7_29416.cif" } resolution = 2.85 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= -0.000 sd= 0.045 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: 6 Type Number sf(0) Gaussians P 71 5.49 5 Mg 4 5.21 5 S 114 5.16 5 C 13864 2.51 5 N 3819 2.21 5 O 4323 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22195 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3580 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 421} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2503 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain: "C" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2586 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain: "D" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2616 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "E" Number of atoms: 2668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2668 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 323} Chain breaks: 1 Chain: "F" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2276 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain breaks: 6 Chain: "G" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2315 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 5, 'TRANS': 286} Chain breaks: 2 Chain: "H" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2330 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 10, 'TRANS': 278} Chain breaks: 4 Chain: "I" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 652 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain breaks: 1 Chain: "J" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 313 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "K" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 201 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.69, per 1000 atoms: 0.21 Number of scatterers: 22195 At special positions: 0 Unit cell: (113.436, 120.888, 139.932, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 114 16.00 P 71 15.00 Mg 4 11.99 O 4323 8.00 N 3819 7.00 C 13864 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: 1.80 Conformation dependent library (CDL) restraints added in 765.2 milliseconds 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5004 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 16 sheets defined 52.1% alpha, 16.9% beta 22 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.557A pdb=" N GLN A 77 " --> pdb=" O CYS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 96 removed outlier: 3.643A pdb=" N ALA A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 131 removed outlier: 3.560A pdb=" N VAL A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 194 through 210 Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 269 through 284 Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 296 through 308 removed outlier: 3.612A pdb=" N VAL A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 373 through 384 removed outlier: 3.850A pdb=" N LYS A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 393 through 408 removed outlier: 3.572A pdb=" N ALA A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.557A pdb=" N ASN A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 468 Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 486 through 499 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 19 through 23 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'B' and resid 69 through 72 removed outlier: 3.832A pdb=" N ALA B 72 " --> pdb=" O ARG B 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 69 through 72' Processing helix chain 'B' and resid 85 through 99 Processing helix chain 'B' and resid 116 through 119 removed outlier: 3.504A pdb=" N MET B 119 " --> pdb=" O ALA B 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 116 through 119' Processing helix chain 'B' and resid 120 through 134 Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.659A pdb=" N LYS B 149 " --> pdb=" O GLN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.927A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 217 Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 244 through 257 Processing helix chain 'B' and resid 262 through 276 Processing helix chain 'B' and resid 281 through 302 Processing helix chain 'B' and resid 305 through 322 removed outlier: 3.833A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 13 removed outlier: 3.725A pdb=" N LEU C 13 " --> pdb=" O LYS C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 27 Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'C' and resid 58 through 71 Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 89 through 101 removed outlier: 3.927A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 123 through 137 removed outlier: 4.111A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.733A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 Processing helix chain 'C' and resid 170 through 186 removed outlier: 3.508A pdb=" N ILE C 174 " --> pdb=" O PRO C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.555A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.598A pdb=" N VAL C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 271 removed outlier: 4.049A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 3.912A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 313 removed outlier: 3.794A pdb=" N VAL C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 332 Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 42 through 55 removed outlier: 3.572A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 91 Proline residue: D 85 - end of helix removed outlier: 4.617A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.744A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 146 through 160 removed outlier: 4.371A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 193 through 208 removed outlier: 5.257A pdb=" N ASP D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ARG D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 224 Processing helix chain 'D' and resid 227 through 246 removed outlier: 3.809A pdb=" N GLY D 231 " --> pdb=" O ASP D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 264 through 277 Processing helix chain 'D' and resid 279 through 292 Processing helix chain 'D' and resid 296 through 311 Processing helix chain 'D' and resid 315 through 334 Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 12 through 16 Processing helix chain 'E' and resid 20 through 32 removed outlier: 4.469A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 36 Processing helix chain 'E' and resid 48 through 62 Processing helix chain 'E' and resid 104 through 118 removed outlier: 3.881A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE E 109 " --> pdb=" O ASP E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 146 removed outlier: 3.800A pdb=" N LEU E 146 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 161 removed outlier: 4.027A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 194 through 209 Processing helix chain 'E' and resid 216 through 226 removed outlier: 3.581A pdb=" N LYS E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 292 Processing helix chain 'E' and resid 295 through 309 Processing helix chain 'E' and resid 314 through 334 Processing helix chain 'E' and resid 337 through 354 removed outlier: 4.427A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 30 removed outlier: 3.663A pdb=" N TYR F 16 " --> pdb=" O ALA F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 77 No H-bonds generated for 'chain 'F' and resid 75 through 77' Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'F' and resid 96 through 113 removed outlier: 3.518A pdb=" N LEU F 100 " --> pdb=" O ASN F 96 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET F 111 " --> pdb=" O TYR F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 219 Processing helix chain 'F' and resid 240 through 252 removed outlier: 4.404A pdb=" N SER F 244 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ALA F 245 " --> pdb=" O GLU F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 425 removed outlier: 3.617A pdb=" N ALA F 424 " --> pdb=" O LYS F 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 27 removed outlier: 3.716A pdb=" N ILE G 21 " --> pdb=" O HIS G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'G' and resid 86 through 93 Processing helix chain 'G' and resid 160 through 173 Processing helix chain 'G' and resid 239 through 243 Processing helix chain 'G' and resid 244 through 246 No H-bonds generated for 'chain 'G' and resid 244 through 246' Processing helix chain 'G' and resid 318 through 330 removed outlier: 4.067A pdb=" N THR G 322 " --> pdb=" O GLU G 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 27 Processing helix chain 'H' and resid 98 through 103 Processing helix chain 'H' and resid 234 through 244 Processing helix chain 'H' and resid 326 through 336 removed outlier: 4.075A pdb=" N GLY H 336 " --> pdb=" O PHE H 332 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 339 No H-bonds generated for 'chain 'H' and resid 337 through 339' Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 removed outlier: 6.131A pdb=" N ILE A 184 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N CYS A 222 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE A 186 " --> pdb=" O CYS A 222 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N THR A 224 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER A 108 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 Processing sheet with id=AA3, first strand: chain 'B' and resid 109 through 114 removed outlier: 6.235A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N TYR B 163 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N SER B 48 " --> pdb=" O TYR B 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.052A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 188 through 189 removed outlier: 7.127A pdb=" N LYS C 188 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.197A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 93 through 96 removed outlier: 6.066A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU E 40 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 69 through 75 Processing sheet with id=AA9, first strand: chain 'F' and resid 79 through 83 removed outlier: 3.911A pdb=" N LEU F 79 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU F 3 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS F 122 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL F 207 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU F 68 " --> pdb=" O SER F 46 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU F 427 " --> pdb=" O SER F 443 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL F 428 " --> pdb=" O LEU F 235 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 79 through 83 removed outlier: 3.911A pdb=" N LEU F 79 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU F 3 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS F 122 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL F 207 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER H 283 " --> pdb=" O LYS F 206 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU H 251 " --> pdb=" O PHE H 266 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 405 through 406 Processing sheet with id=AB3, first strand: chain 'F' and resid 405 through 406 removed outlier: 3.591A pdb=" N ARG G 129 " --> pdb=" O GLU F 293 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 80 through 85 removed outlier: 7.189A pdb=" N ASP G 36 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLU G 51 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE G 48 " --> pdb=" O LEU G 60 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE G 56 " --> pdb=" O ASN G 52 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL G 305 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE G 304 " --> pdb=" O SER G 271 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER G 271 " --> pdb=" O ILE G 304 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE G 306 " --> pdb=" O ILE G 269 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL G 264 " --> pdb=" O ASP G 260 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS G 216 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LYS G 159 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU G 214 " --> pdb=" O LYS G 159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 232 through 238 removed outlier: 4.633A pdb=" N PHE G 192 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS G 204 " --> pdb=" O GLU H 147 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE H 3 " --> pdb=" O VAL H 120 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 78 through 80 Processing sheet with id=AB7, first strand: chain 'H' and resid 78 through 80 removed outlier: 7.174A pdb=" N ASP H 29 " --> pdb=" O MET H 44 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N MET H 44 " --> pdb=" O ASP H 29 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLN H 365 " --> pdb=" O ASN H 348 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN H 348 " --> pdb=" O GLN H 365 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE H 353 " --> pdb=" O ASN H 228 " (cutoff:3.500A) 1182 hydrogen bonds defined for protein. 3396 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 3.31 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 7207 1.36 - 1.51: 6083 1.51 - 1.66: 9230 1.66 - 1.80: 79 1.80 - 1.95: 90 Bond restraints: 22689 Sorted by residual: bond pdb=" N SER E 90 " pdb=" CA SER E 90 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.04e-02 9.25e+03 8.84e+00 bond pdb=" N HIS E 93 " pdb=" CA HIS E 93 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.21e-02 6.83e+03 8.09e+00 bond pdb=" N VAL D 256 " pdb=" CA VAL D 256 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 8.01e+00 bond pdb=" C3' DT I 19 " pdb=" C2' DT I 19 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.73e+00 bond pdb=" N VAL D 262 " pdb=" CA VAL D 262 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.17e-02 7.31e+03 7.66e+00 ... (remaining 22684 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 30370 2.02 - 4.05: 479 4.05 - 6.07: 48 6.07 - 8.09: 9 8.09 - 10.12: 3 Bond angle restraints: 30909 Sorted by residual: angle pdb=" N3 DT K 3 " pdb=" C4 DT K 3 " pdb=" O4 DT K 3 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT J 8 " pdb=" C4 DT J 8 " pdb=" O4 DT J 8 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT K 7 " pdb=" C4 DT K 7 " pdb=" O4 DT K 7 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT K 4 " pdb=" C4 DT K 4 " pdb=" O4 DT K 4 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT I 22 " pdb=" C4 DT I 22 " pdb=" O4 DT I 22 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 ... (remaining 30904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.71: 12701 31.71 - 63.43: 942 63.43 - 95.14: 32 95.14 - 126.85: 1 126.85 - 158.57: 2 Dihedral angle restraints: 13678 sinusoidal: 6002 harmonic: 7676 Sorted by residual: dihedral pdb=" C5' ADP E 500 " pdb=" O5' ADP E 500 " pdb=" PA ADP E 500 " pdb=" O2A ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 98.57 -158.57 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" O2A ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PA ADP E 500 " pdb=" PB ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 72.96 -132.96 1 2.00e+01 2.50e-03 4.04e+01 dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 64.39 -124.39 1 2.00e+01 2.50e-03 3.76e+01 ... (remaining 13675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2406 0.036 - 0.071: 823 0.071 - 0.107: 249 0.107 - 0.143: 84 0.143 - 0.178: 12 Chirality restraints: 3574 Sorted by residual: chirality pdb=" CA ILE F 468 " pdb=" N ILE F 468 " pdb=" C ILE F 468 " pdb=" CB ILE F 468 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.94e-01 chirality pdb=" CA VAL E 88 " pdb=" N VAL E 88 " pdb=" C VAL E 88 " pdb=" CB VAL E 88 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CB ILE E 211 " pdb=" CA ILE E 211 " pdb=" CG1 ILE E 211 " pdb=" CG2 ILE E 211 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.80e-01 ... (remaining 3571 not shown) Planarity restraints: 3695 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 217 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C LEU D 217 " -0.055 2.00e-02 2.50e+03 pdb=" O LEU D 217 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU D 218 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY E 62 " 0.052 5.00e-02 4.00e+02 7.86e-02 9.88e+00 pdb=" N PRO E 63 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO E 63 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 63 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 97 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO E 98 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 98 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 98 " -0.035 5.00e-02 4.00e+02 ... (remaining 3692 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 254 2.63 - 3.20: 18985 3.20 - 3.77: 35787 3.77 - 4.33: 49329 4.33 - 4.90: 81329 Nonbonded interactions: 185684 Sorted by model distance: nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 2.068 2.170 nonbonded pdb="MG MG C 401 " pdb=" O2G AGS C 402 " model vdw 2.070 2.170 nonbonded pdb=" OG1 THR C 60 " pdb="MG MG C 401 " model vdw 2.075 2.170 nonbonded pdb=" OG1 THR B 56 " pdb="MG MG B 402 " model vdw 2.078 2.170 nonbonded pdb=" O3G AGS D 401 " pdb="MG MG D 402 " model vdw 2.098 2.170 ... (remaining 185679 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 6.610 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: 0.040 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 20.820 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22689 Z= 0.229 Angle : 0.585 10.118 30909 Z= 0.375 Chirality : 0.042 0.178 3574 Planarity : 0.004 0.079 3695 Dihedral : 18.871 158.569 8674 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.37 % Allowed : 25.66 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.17), residues: 2570 helix: 1.16 (0.15), residues: 1235 sheet: 0.25 (0.24), residues: 548 loop : -0.40 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 230 TYR 0.025 0.001 TYR B 186 PHE 0.012 0.001 PHE H 152 TRP 0.013 0.001 TRP E 259 HIS 0.006 0.001 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.23 (22689) covalent geometry : angle 0.58503 / 0.38 (30909) hydrogen bonds : bond 0.17236 / 11.22 ( 1209) hydrogen bonds : angle 6.91896 / 5.00 ( 3506) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 288 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 284 ASN cc_start: 0.7204 (m-40) cc_final: 0.6977 (m110) REVERT: C 87 ASP cc_start: 0.7902 (t70) cc_final: 0.7647 (t0) REVERT: F 41 ARG cc_start: 0.5911 (OUTLIER) cc_final: 0.5591 (ptp-110) REVERT: F 470 ARG cc_start: 0.7572 (ptt90) cc_final: 0.7348 (ptt180) REVERT: G 151 ARG cc_start: 0.7635 (tpp80) cc_final: 0.7389 (mpp80) REVERT: G 202 PHE cc_start: 0.7272 (OUTLIER) cc_final: 0.6840 (m-80) REVERT: H 45 ASN cc_start: 0.7840 (t0) cc_final: 0.7613 (t0) REVERT: H 63 GLU cc_start: 0.6965 (pm20) cc_final: 0.6577 (pm20) REVERT: H 250 ASP cc_start: 0.7759 (p0) cc_final: 0.7555 (p0) REVERT: H 284 MET cc_start: 0.7030 (ttt) cc_final: 0.6811 (ttm) outliers start: 56 outliers final: 43 residues processed: 338 average time/residue: 0.5252 time to fit residues: 206.3443 Evaluate side-chains 306 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 261 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 118 ASN Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 322 ILE Chi-restraints excluded: chain H residue 369 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN C 74 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.176161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.141632 restraints weight = 24545.723| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 1.71 r_work: 0.3544 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22689 Z= 0.125 Angle : 0.532 9.154 30909 Z= 0.284 Chirality : 0.041 0.159 3574 Planarity : 0.004 0.057 3695 Dihedral : 16.138 177.439 3526 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.26 % Rotamer: Outliers : 4.23 % Allowed : 22.53 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.17), residues: 2570 helix: 1.48 (0.15), residues: 1247 sheet: 0.31 (0.23), residues: 538 loop : -0.29 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 214 TYR 0.015 0.001 TYR A 235 PHE 0.023 0.001 PHE G 40 TRP 0.007 0.001 TRP D 324 HIS 0.005 0.001 HIS H 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (22689) covalent geometry : angle 0.53171 / 0.28 (30909) hydrogen bonds : bond 0.04318 / 2.79 ( 1209) hydrogen bonds : angle 5.07881 / 3.62 ( 3506) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 277 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 227 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8112 (tt0) REVERT: A 286 LYS cc_start: 0.8385 (mtmt) cc_final: 0.8103 (ttpp) REVERT: A 296 LYS cc_start: 0.7670 (mptt) cc_final: 0.7450 (mtpp) REVERT: A 307 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6992 (mt-10) REVERT: A 354 ASN cc_start: 0.8470 (m-40) cc_final: 0.8241 (t0) REVERT: A 375 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7314 (t0) REVERT: A 497 TYR cc_start: 0.5430 (OUTLIER) cc_final: 0.5214 (p90) REVERT: B 48 SER cc_start: 0.8790 (OUTLIER) cc_final: 0.8583 (p) REVERT: B 148 ASN cc_start: 0.7943 (OUTLIER) cc_final: 0.7559 (p0) REVERT: B 183 ASP cc_start: 0.8105 (t70) cc_final: 0.7478 (t0) REVERT: B 291 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: C 87 ASP cc_start: 0.8074 (t70) cc_final: 0.7831 (t0) REVERT: C 94 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7932 (mtp180) REVERT: C 167 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8526 (pt0) REVERT: D 111 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8144 (ttmt) REVERT: D 178 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7673 (t0) REVERT: D 207 GLN cc_start: 0.8349 (mp10) cc_final: 0.8046 (mm-40) REVERT: F 31 LYS cc_start: 0.7847 (ptmt) cc_final: 0.7537 (pmtt) REVERT: F 41 ARG cc_start: 0.5654 (OUTLIER) cc_final: 0.5218 (ptp-110) REVERT: F 224 MET cc_start: 0.6335 (OUTLIER) cc_final: 0.5775 (mmt) REVERT: F 232 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.8052 (mpp) REVERT: F 470 ARG cc_start: 0.7654 (ptt90) cc_final: 0.7448 (ptt180) REVERT: G 159 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7943 (ptmm) REVERT: H 55 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8469 (mtm180) REVERT: H 284 MET cc_start: 0.7658 (ttt) cc_final: 0.7447 (ttm) outliers start: 100 outliers final: 41 residues processed: 347 average time/residue: 0.5069 time to fit residues: 203.8537 Evaluate side-chains 302 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 247 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 190 ASN Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 322 ILE Chi-restraints excluded: chain H residue 350 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 chunk 206 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 205 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 203 optimal weight: 0.9980 chunk 255 optimal weight: 0.2980 chunk 145 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN C 77 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN H 243 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.175288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.139628 restraints weight = 24926.180| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.00 r_work: 0.3493 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22689 Z= 0.112 Angle : 0.500 7.709 30909 Z= 0.267 Chirality : 0.040 0.160 3574 Planarity : 0.004 0.046 3695 Dihedral : 15.914 156.232 3486 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.50 % Favored : 96.46 % Rotamer: Outliers : 4.23 % Allowed : 22.49 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.17), residues: 2570 helix: 1.63 (0.15), residues: 1249 sheet: 0.31 (0.23), residues: 538 loop : -0.23 (0.24), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 214 TYR 0.014 0.001 TYR A 235 PHE 0.021 0.001 PHE G 202 TRP 0.007 0.001 TRP D 324 HIS 0.006 0.001 HIS E 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (22689) covalent geometry : angle 0.50025 / 0.27 (30909) hydrogen bonds : bond 0.03789 / 2.45 ( 1209) hydrogen bonds : angle 4.66903 / 3.33 ( 3506) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 268 time to evaluate : 0.754 Fit side-chains REVERT: A 227 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8024 (tt0) REVERT: A 354 ASN cc_start: 0.8517 (m-40) cc_final: 0.8262 (t0) REVERT: A 497 TYR cc_start: 0.5503 (OUTLIER) cc_final: 0.5190 (p90) REVERT: B 183 ASP cc_start: 0.8019 (t70) cc_final: 0.7399 (t0) REVERT: B 291 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7485 (mp0) REVERT: C 87 ASP cc_start: 0.8027 (t70) cc_final: 0.7772 (t0) REVERT: C 94 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7991 (mtp180) REVERT: C 167 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8557 (pt0) REVERT: C 305 ASP cc_start: 0.8062 (m-30) cc_final: 0.7800 (m-30) REVERT: D 111 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8149 (ttmt) REVERT: E 34 ARG cc_start: 0.7472 (mmp-170) cc_final: 0.6662 (mmm-85) REVERT: E 221 ARG cc_start: 0.7248 (mtp85) cc_final: 0.6858 (mtp-110) REVERT: F 31 LYS cc_start: 0.7878 (ptmt) cc_final: 0.7544 (pmtt) REVERT: F 71 THR cc_start: 0.7901 (m) cc_final: 0.7589 (p) REVERT: F 224 MET cc_start: 0.6396 (OUTLIER) cc_final: 0.5817 (mmt) REVERT: F 232 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.8057 (mpp) REVERT: G 61 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7611 (mp) REVERT: G 159 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8048 (ptmm) REVERT: H 55 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8573 (mtm180) REVERT: H 284 MET cc_start: 0.7808 (ttt) cc_final: 0.7561 (ttm) REVERT: H 346 ASN cc_start: 0.4581 (OUTLIER) cc_final: 0.3023 (t0) REVERT: H 348 ASN cc_start: 0.7291 (p0) cc_final: 0.6867 (p0) REVERT: H 364 MET cc_start: 0.8519 (mtm) cc_final: 0.8292 (mtp) outliers start: 100 outliers final: 41 residues processed: 341 average time/residue: 0.5400 time to fit residues: 212.9179 Evaluate side-chains 287 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 235 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 190 ASN Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 322 ILE Chi-restraints excluded: chain H residue 346 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 160 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 242 optimal weight: 1.9990 chunk 238 optimal weight: 0.0070 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN E 19 ASN E 141 ASN E 227 ASN H 233 ASN H 286 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.172571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.136522 restraints weight = 24921.198| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.88 r_work: 0.3440 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22689 Z= 0.141 Angle : 0.519 8.939 30909 Z= 0.276 Chirality : 0.041 0.153 3574 Planarity : 0.004 0.046 3695 Dihedral : 15.836 137.979 3474 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.85 % Favored : 96.11 % Rotamer: Outliers : 4.78 % Allowed : 22.10 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.17), residues: 2570 helix: 1.62 (0.15), residues: 1250 sheet: 0.33 (0.22), residues: 540 loop : -0.26 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 86 TYR 0.012 0.001 TYR A 235 PHE 0.017 0.001 PHE A 201 TRP 0.009 0.001 TRP D 324 HIS 0.006 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (22689) covalent geometry : angle 0.51944 / 0.28 (30909) hydrogen bonds : bond 0.03884 / 2.50 ( 1209) hydrogen bonds : angle 4.50730 / 3.21 ( 3506) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 253 time to evaluate : 0.852 Fit side-chains REVERT: A 227 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8006 (tt0) REVERT: A 497 TYR cc_start: 0.5518 (OUTLIER) cc_final: 0.5298 (p90) REVERT: B 100 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8487 (tmtt) REVERT: B 183 ASP cc_start: 0.8082 (t70) cc_final: 0.7455 (t0) REVERT: B 291 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: C 87 ASP cc_start: 0.8086 (t70) cc_final: 0.7826 (t0) REVERT: C 94 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8021 (mtp180) REVERT: C 167 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8599 (pt0) REVERT: D 254 THR cc_start: 0.8151 (OUTLIER) cc_final: 0.7830 (t) REVERT: E 251 SER cc_start: 0.8513 (t) cc_final: 0.8185 (m) REVERT: F 31 LYS cc_start: 0.7874 (ptmt) cc_final: 0.7539 (pmtt) REVERT: F 71 THR cc_start: 0.7913 (m) cc_final: 0.7552 (p) REVERT: F 88 LEU cc_start: 0.6338 (tp) cc_final: 0.6088 (tm) REVERT: F 224 MET cc_start: 0.6398 (OUTLIER) cc_final: 0.5828 (mmt) REVERT: G 61 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7733 (mp) REVERT: G 159 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8057 (ptmm) REVERT: H 55 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8477 (mtm180) REVERT: H 284 MET cc_start: 0.7782 (ttt) cc_final: 0.7198 (mtp) REVERT: H 346 ASN cc_start: 0.4674 (OUTLIER) cc_final: 0.3124 (t0) REVERT: H 348 ASN cc_start: 0.7309 (p0) cc_final: 0.6679 (p0) REVERT: H 364 MET cc_start: 0.8551 (mtm) cc_final: 0.8302 (mtp) outliers start: 113 outliers final: 57 residues processed: 336 average time/residue: 0.5394 time to fit residues: 211.0681 Evaluate side-chains 312 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 244 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 190 ASN Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 322 ILE Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 346 ASN Chi-restraints excluded: chain H residue 362 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 25 optimal weight: 0.6980 chunk 177 optimal weight: 9.9990 chunk 156 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 234 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 249 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 ASN A 202 GLN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN C 77 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN E 227 ASN F 291 HIS H 100 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.170015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.133430 restraints weight = 24472.801| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.84 r_work: 0.3408 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22689 Z= 0.151 Angle : 0.527 8.036 30909 Z= 0.279 Chirality : 0.042 0.162 3574 Planarity : 0.004 0.052 3695 Dihedral : 15.877 124.954 3474 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.77 % Favored : 96.19 % Rotamer: Outliers : 4.65 % Allowed : 22.40 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.17), residues: 2570 helix: 1.56 (0.15), residues: 1252 sheet: 0.36 (0.22), residues: 538 loop : -0.28 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 230 TYR 0.021 0.001 TYR B 186 PHE 0.019 0.001 PHE G 202 TRP 0.009 0.001 TRP D 324 HIS 0.007 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (22689) covalent geometry : angle 0.52728 / 0.28 (30909) hydrogen bonds : bond 0.03971 / 2.56 ( 1209) hydrogen bonds : angle 4.44083 / 3.15 ( 3506) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 252 time to evaluate : 0.854 Fit side-chains REVERT: A 225 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.7716 (mt-10) REVERT: A 227 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7988 (tt0) REVERT: A 296 LYS cc_start: 0.7643 (mptt) cc_final: 0.7381 (mtpt) REVERT: A 307 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6890 (mt-10) REVERT: B 48 SER cc_start: 0.8896 (OUTLIER) cc_final: 0.8430 (m) REVERT: B 100 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8554 (tmtt) REVERT: B 183 ASP cc_start: 0.8220 (t70) cc_final: 0.7616 (t0) REVERT: B 291 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: C 94 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8027 (mtp180) REVERT: C 167 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8592 (pt0) REVERT: D 111 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8152 (ttmt) REVERT: D 211 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7104 (mttp) REVERT: E 34 ARG cc_start: 0.7497 (mmp-170) cc_final: 0.6658 (mmm-85) REVERT: E 251 SER cc_start: 0.8498 (t) cc_final: 0.8155 (m) REVERT: F 31 LYS cc_start: 0.7827 (ptmt) cc_final: 0.7480 (pmtt) REVERT: F 71 THR cc_start: 0.7917 (m) cc_final: 0.7538 (p) REVERT: F 99 SER cc_start: 0.7640 (m) cc_final: 0.7166 (t) REVERT: F 224 MET cc_start: 0.6362 (OUTLIER) cc_final: 0.5768 (mmt) REVERT: F 232 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7091 (mpt) REVERT: G 10 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7871 (mtpp) REVERT: G 61 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7829 (mp) REVERT: H 55 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8474 (mtm180) REVERT: H 284 MET cc_start: 0.7770 (ttt) cc_final: 0.7247 (mtp) REVERT: H 346 ASN cc_start: 0.4702 (OUTLIER) cc_final: 0.3179 (t0) REVERT: H 348 ASN cc_start: 0.7327 (p0) cc_final: 0.6667 (p0) outliers start: 110 outliers final: 57 residues processed: 334 average time/residue: 0.5288 time to fit residues: 204.7046 Evaluate side-chains 322 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 251 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 190 ASN Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 346 ASN Chi-restraints excluded: chain H residue 362 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 162 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 203 optimal weight: 0.9980 chunk 240 optimal weight: 6.9990 chunk 197 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN C 77 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN D 35 ASN E 110 GLN E 227 ASN ** H 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.169889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.133321 restraints weight = 24698.468| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.86 r_work: 0.3407 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22689 Z= 0.142 Angle : 0.523 9.662 30909 Z= 0.276 Chirality : 0.042 0.155 3574 Planarity : 0.004 0.048 3695 Dihedral : 15.882 126.358 3472 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.77 % Favored : 96.19 % Rotamer: Outliers : 5.07 % Allowed : 22.65 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.17), residues: 2570 helix: 1.55 (0.15), residues: 1252 sheet: 0.36 (0.22), residues: 538 loop : -0.27 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 9 TYR 0.013 0.001 TYR A 175 PHE 0.015 0.001 PHE G 202 TRP 0.010 0.001 TRP D 324 HIS 0.007 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (22689) covalent geometry : angle 0.52260 / 0.28 (30909) hydrogen bonds : bond 0.03862 / 2.48 ( 1209) hydrogen bonds : angle 4.38509 / 3.11 ( 3506) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 260 time to evaluate : 0.996 Fit side-chains REVERT: A 89 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: A 225 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.7732 (mt-10) REVERT: A 227 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8010 (tt0) REVERT: A 296 LYS cc_start: 0.7673 (mptt) cc_final: 0.7405 (mttt) REVERT: A 302 ASP cc_start: 0.8071 (m-30) cc_final: 0.7830 (m-30) REVERT: A 307 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6904 (mt-10) REVERT: B 48 SER cc_start: 0.8888 (OUTLIER) cc_final: 0.8424 (m) REVERT: B 100 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8557 (tmtt) REVERT: B 183 ASP cc_start: 0.8219 (t70) cc_final: 0.7610 (t0) REVERT: B 291 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: B 301 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7813 (mt-10) REVERT: C 94 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8067 (mtp180) REVERT: C 167 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8584 (pt0) REVERT: D 111 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8171 (ttmt) REVERT: D 211 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7109 (mttp) REVERT: D 254 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7804 (t) REVERT: E 9 ARG cc_start: 0.8283 (ttm-80) cc_final: 0.8006 (tpt-90) REVERT: E 34 ARG cc_start: 0.7439 (mmp-170) cc_final: 0.6619 (mmm-85) REVERT: E 251 SER cc_start: 0.8530 (t) cc_final: 0.8191 (m) REVERT: F 31 LYS cc_start: 0.7811 (ptmt) cc_final: 0.7467 (pmtt) REVERT: F 71 THR cc_start: 0.7908 (m) cc_final: 0.7553 (p) REVERT: F 99 SER cc_start: 0.7674 (m) cc_final: 0.7188 (t) REVERT: F 224 MET cc_start: 0.6389 (OUTLIER) cc_final: 0.5783 (mmt) REVERT: F 232 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7127 (mpt) REVERT: G 10 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7908 (mtpp) REVERT: G 61 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7867 (mp) REVERT: G 325 GLU cc_start: 0.6972 (pp20) cc_final: 0.6711 (pp20) REVERT: H 55 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8471 (mtm180) REVERT: H 284 MET cc_start: 0.7758 (ttt) cc_final: 0.7276 (mtp) REVERT: H 346 ASN cc_start: 0.4657 (OUTLIER) cc_final: 0.3074 (t0) REVERT: H 348 ASN cc_start: 0.7308 (p0) cc_final: 0.6630 (p0) REVERT: H 364 MET cc_start: 0.8607 (mtm) cc_final: 0.8274 (mtp) outliers start: 120 outliers final: 65 residues processed: 345 average time/residue: 0.5612 time to fit residues: 224.0659 Evaluate side-chains 329 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 247 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 190 ASN Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 346 ASN Chi-restraints excluded: chain H residue 362 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 218 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 221 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 231 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 206 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 ASN A 81 HIS A 203 GLN C 74 ASN C 77 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN D 35 ASN E 208 ASN E 227 ASN F 247 HIS F 263 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.168353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.131711 restraints weight = 24782.520| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.83 r_work: 0.3383 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22689 Z= 0.178 Angle : 0.554 10.178 30909 Z= 0.292 Chirality : 0.043 0.161 3574 Planarity : 0.004 0.049 3695 Dihedral : 15.929 127.619 3472 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.05 % Favored : 95.91 % Rotamer: Outliers : 4.69 % Allowed : 23.33 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.17), residues: 2570 helix: 1.46 (0.15), residues: 1252 sheet: 0.35 (0.22), residues: 539 loop : -0.30 (0.24), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 230 TYR 0.020 0.002 TYR B 186 PHE 0.015 0.002 PHE A 201 TRP 0.010 0.001 TRP D 324 HIS 0.007 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (22689) covalent geometry : angle 0.55442 / 0.29 (30909) hydrogen bonds : bond 0.04169 / 2.68 ( 1209) hydrogen bonds : angle 4.42453 / 3.14 ( 3506) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 253 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 225 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.7792 (mt-10) REVERT: A 227 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7989 (tt0) REVERT: A 296 LYS cc_start: 0.7708 (mptt) cc_final: 0.7427 (mttt) REVERT: A 307 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6902 (mt-10) REVERT: B 48 SER cc_start: 0.8902 (OUTLIER) cc_final: 0.8420 (m) REVERT: B 100 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8551 (tmtt) REVERT: B 183 ASP cc_start: 0.8256 (t70) cc_final: 0.7626 (t0) REVERT: B 291 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: C 94 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8068 (mtp180) REVERT: C 167 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8619 (pt0) REVERT: D 111 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8217 (ttmt) REVERT: D 211 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7151 (mttp) REVERT: D 254 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7807 (t) REVERT: D 279 ASP cc_start: 0.7715 (t70) cc_final: 0.7442 (t0) REVERT: E 9 ARG cc_start: 0.8289 (ttm-80) cc_final: 0.8005 (tpt-90) REVERT: E 34 ARG cc_start: 0.7483 (mmp-170) cc_final: 0.6665 (mmm-85) REVERT: F 224 MET cc_start: 0.6358 (OUTLIER) cc_final: 0.5763 (mmt) REVERT: F 232 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7184 (mpt) REVERT: G 10 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7901 (mtpp) REVERT: G 61 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7895 (mp) REVERT: G 325 GLU cc_start: 0.7044 (pp20) cc_final: 0.6768 (pp20) REVERT: H 284 MET cc_start: 0.7791 (ttt) cc_final: 0.7308 (mtp) REVERT: H 346 ASN cc_start: 0.4704 (OUTLIER) cc_final: 0.3143 (t0) REVERT: H 348 ASN cc_start: 0.7346 (p0) cc_final: 0.6677 (p0) REVERT: H 364 MET cc_start: 0.8644 (mtm) cc_final: 0.8321 (mtp) outliers start: 111 outliers final: 66 residues processed: 336 average time/residue: 0.5897 time to fit residues: 228.7798 Evaluate side-chains 319 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 239 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 322 ILE Chi-restraints excluded: chain H residue 346 ASN Chi-restraints excluded: chain H residue 362 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 173 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 213 optimal weight: 0.7980 chunk 206 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 12 optimal weight: 0.4980 chunk 171 optimal weight: 0.9990 chunk 238 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 ASN C 74 ASN C 77 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN E 208 ASN E 227 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.169496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.132813 restraints weight = 24639.955| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.86 r_work: 0.3406 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22689 Z= 0.126 Angle : 0.523 10.819 30909 Z= 0.276 Chirality : 0.041 0.154 3574 Planarity : 0.004 0.049 3695 Dihedral : 15.885 128.158 3472 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.15 % Rotamer: Outliers : 4.48 % Allowed : 24.01 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.17), residues: 2570 helix: 1.55 (0.15), residues: 1252 sheet: 0.33 (0.22), residues: 539 loop : -0.28 (0.24), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 136 TYR 0.012 0.001 TYR A 175 PHE 0.017 0.001 PHE G 202 TRP 0.010 0.001 TRP D 324 HIS 0.006 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (22689) covalent geometry : angle 0.52323 / 0.28 (30909) hydrogen bonds : bond 0.03755 / 2.42 ( 1209) hydrogen bonds : angle 4.34277 / 3.08 ( 3506) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 247 time to evaluate : 0.799 Fit side-chains REVERT: A 89 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7760 (tt0) REVERT: A 225 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.7747 (mt-10) REVERT: A 227 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7979 (tt0) REVERT: A 296 LYS cc_start: 0.7751 (mptt) cc_final: 0.7449 (mttt) REVERT: A 302 ASP cc_start: 0.8042 (m-30) cc_final: 0.7778 (m-30) REVERT: A 307 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6936 (mt-10) REVERT: B 48 SER cc_start: 0.8894 (OUTLIER) cc_final: 0.8429 (m) REVERT: B 100 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8556 (tmtt) REVERT: B 183 ASP cc_start: 0.8223 (t70) cc_final: 0.7610 (t0) REVERT: B 197 THR cc_start: 0.8817 (m) cc_final: 0.8486 (p) REVERT: B 291 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: C 167 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8558 (pt0) REVERT: D 211 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7139 (mttp) REVERT: D 254 THR cc_start: 0.8132 (OUTLIER) cc_final: 0.7816 (t) REVERT: D 279 ASP cc_start: 0.7684 (t70) cc_final: 0.7406 (t0) REVERT: E 9 ARG cc_start: 0.8280 (ttm-80) cc_final: 0.8025 (tpt-90) REVERT: E 34 ARG cc_start: 0.7480 (mmp-170) cc_final: 0.6660 (mmm-85) REVERT: F 224 MET cc_start: 0.6370 (OUTLIER) cc_final: 0.5766 (mmt) REVERT: F 232 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7858 (tpp) REVERT: G 10 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7904 (mtpp) REVERT: G 61 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7880 (mp) REVERT: G 159 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7943 (ptmm) REVERT: G 161 GLU cc_start: 0.7390 (mp0) cc_final: 0.6757 (mp0) REVERT: G 325 GLU cc_start: 0.6987 (pp20) cc_final: 0.6735 (pp20) REVERT: H 284 MET cc_start: 0.7768 (ttt) cc_final: 0.7303 (mtp) REVERT: H 346 ASN cc_start: 0.4686 (OUTLIER) cc_final: 0.3123 (t0) REVERT: H 348 ASN cc_start: 0.7320 (p0) cc_final: 0.6606 (p0) REVERT: H 364 MET cc_start: 0.8618 (mtm) cc_final: 0.8376 (mtp) outliers start: 106 outliers final: 62 residues processed: 330 average time/residue: 0.5845 time to fit residues: 223.9234 Evaluate side-chains 313 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 237 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 322 ILE Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 346 ASN Chi-restraints excluded: chain H residue 362 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 23 optimal weight: 4.9990 chunk 232 optimal weight: 2.9990 chunk 37 optimal weight: 0.0670 chunk 115 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 237 optimal weight: 3.9990 chunk 216 optimal weight: 0.0670 chunk 68 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 202 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 ASN B 146 GLN C 74 ASN C 77 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN E 227 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.172294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.136904 restraints weight = 24710.897| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.77 r_work: 0.3461 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22689 Z= 0.126 Angle : 0.522 11.385 30909 Z= 0.276 Chirality : 0.041 0.156 3574 Planarity : 0.004 0.048 3695 Dihedral : 15.851 128.597 3471 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.89 % Favored : 96.07 % Rotamer: Outliers : 3.97 % Allowed : 24.43 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.17), residues: 2570 helix: 1.58 (0.15), residues: 1253 sheet: 0.33 (0.22), residues: 545 loop : -0.23 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 230 TYR 0.011 0.001 TYR G 181 PHE 0.013 0.001 PHE A 201 TRP 0.010 0.001 TRP D 324 HIS 0.006 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (22689) covalent geometry : angle 0.52206 / 0.28 (30909) hydrogen bonds : bond 0.03672 / 2.36 ( 1209) hydrogen bonds : angle 4.29017 / 3.04 ( 3506) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 246 time to evaluate : 0.910 Fit side-chains REVERT: A 89 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: A 225 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.7664 (mt-10) REVERT: A 227 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8020 (tt0) REVERT: A 296 LYS cc_start: 0.7791 (mptt) cc_final: 0.7495 (mttt) REVERT: A 307 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6932 (mt-10) REVERT: B 48 SER cc_start: 0.8861 (OUTLIER) cc_final: 0.8408 (m) REVERT: B 100 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8552 (tmtt) REVERT: B 183 ASP cc_start: 0.8210 (t70) cc_final: 0.7596 (t0) REVERT: B 197 THR cc_start: 0.8843 (m) cc_final: 0.8545 (p) REVERT: B 291 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: C 167 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8571 (pt0) REVERT: D 211 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7197 (mttp) REVERT: D 254 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7877 (t) REVERT: D 279 ASP cc_start: 0.7747 (t70) cc_final: 0.7490 (t0) REVERT: E 9 ARG cc_start: 0.8237 (ttm-80) cc_final: 0.8017 (tpt-90) REVERT: E 34 ARG cc_start: 0.7445 (mmp-170) cc_final: 0.6658 (mmm-85) REVERT: F 224 MET cc_start: 0.6411 (OUTLIER) cc_final: 0.5805 (mmt) REVERT: F 232 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7897 (tpp) REVERT: G 10 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7983 (mtpp) REVERT: G 61 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7873 (mp) REVERT: G 159 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7944 (ptmm) REVERT: G 161 GLU cc_start: 0.7408 (mp0) cc_final: 0.6779 (mp0) REVERT: G 169 ASP cc_start: 0.7860 (t0) cc_final: 0.7542 (t70) REVERT: H 55 ARG cc_start: 0.8882 (mtm-85) cc_final: 0.8602 (mtm180) REVERT: H 284 MET cc_start: 0.7786 (ttt) cc_final: 0.7376 (mtp) REVERT: H 346 ASN cc_start: 0.4729 (OUTLIER) cc_final: 0.3187 (t0) REVERT: H 348 ASN cc_start: 0.7294 (p0) cc_final: 0.6599 (p0) REVERT: H 364 MET cc_start: 0.8632 (mtm) cc_final: 0.8318 (mtp) outliers start: 94 outliers final: 58 residues processed: 319 average time/residue: 0.5752 time to fit residues: 213.4519 Evaluate side-chains 314 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 242 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 322 ILE Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 346 ASN Chi-restraints excluded: chain H residue 362 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 149 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 240 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 210 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 159 optimal weight: 0.6980 chunk 150 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 ASN B 146 GLN C 74 ASN C 77 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS C 292 ASN E 227 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.172159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.136679 restraints weight = 24813.222| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.78 r_work: 0.3463 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22689 Z= 0.125 Angle : 0.529 14.070 30909 Z= 0.277 Chirality : 0.041 0.188 3574 Planarity : 0.004 0.048 3695 Dihedral : 15.841 129.139 3471 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.23 % Rotamer: Outliers : 3.51 % Allowed : 25.06 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.17), residues: 2570 helix: 1.62 (0.15), residues: 1250 sheet: 0.34 (0.22), residues: 544 loop : -0.21 (0.24), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 136 TYR 0.022 0.001 TYR B 186 PHE 0.012 0.001 PHE A 201 TRP 0.010 0.001 TRP D 324 HIS 0.006 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (22689) covalent geometry : angle 0.52861 / 0.28 (30909) hydrogen bonds : bond 0.03627 / 2.33 ( 1209) hydrogen bonds : angle 4.27079 / 3.03 ( 3506) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 249 time to evaluate : 0.861 Fit side-chains REVERT: A 89 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7839 (tt0) REVERT: A 225 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.7662 (mt-10) REVERT: A 227 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8044 (tt0) REVERT: A 296 LYS cc_start: 0.7819 (mptt) cc_final: 0.7541 (mtpt) REVERT: A 307 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6970 (mt-10) REVERT: B 48 SER cc_start: 0.8853 (OUTLIER) cc_final: 0.8405 (m) REVERT: B 100 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8577 (tmtt) REVERT: B 183 ASP cc_start: 0.8221 (t70) cc_final: 0.7619 (t0) REVERT: B 197 THR cc_start: 0.8855 (m) cc_final: 0.8554 (p) REVERT: B 291 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: C 87 ASP cc_start: 0.8058 (t70) cc_final: 0.7803 (t0) REVERT: C 167 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8569 (pt0) REVERT: D 211 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7207 (mttp) REVERT: D 254 THR cc_start: 0.8088 (OUTLIER) cc_final: 0.7814 (t) REVERT: D 279 ASP cc_start: 0.7722 (t70) cc_final: 0.7469 (t0) REVERT: E 9 ARG cc_start: 0.8222 (ttm-80) cc_final: 0.8020 (tpt-90) REVERT: E 163 LYS cc_start: 0.8637 (tttt) cc_final: 0.8030 (ttpt) REVERT: F 224 MET cc_start: 0.6408 (OUTLIER) cc_final: 0.5797 (mmt) REVERT: F 232 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7906 (tpp) REVERT: G 10 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7997 (mtpp) REVERT: G 61 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7877 (mp) REVERT: G 159 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.7916 (ptmm) REVERT: G 161 GLU cc_start: 0.7444 (mp0) cc_final: 0.6833 (mp0) REVERT: H 55 ARG cc_start: 0.8879 (mtm-85) cc_final: 0.8601 (mtm180) REVERT: H 255 GLU cc_start: 0.7378 (pm20) cc_final: 0.6899 (pp20) REVERT: H 284 MET cc_start: 0.7806 (ttt) cc_final: 0.7406 (mtp) REVERT: H 346 ASN cc_start: 0.4716 (OUTLIER) cc_final: 0.3192 (t0) REVERT: H 348 ASN cc_start: 0.7300 (p0) cc_final: 0.6615 (p0) REVERT: H 364 MET cc_start: 0.8631 (mtm) cc_final: 0.8399 (mtp) outliers start: 83 outliers final: 54 residues processed: 312 average time/residue: 0.5467 time to fit residues: 198.2553 Evaluate side-chains 308 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 240 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 322 ILE Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 346 ASN Chi-restraints excluded: chain H residue 362 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 110 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 206 optimal weight: 3.9990 chunk 253 optimal weight: 0.0980 chunk 138 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 260 optimal weight: 40.0000 chunk 137 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 ASN B 146 GLN C 74 ASN C 77 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN E 227 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.172940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.137423 restraints weight = 24671.810| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.80 r_work: 0.3470 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22689 Z= 0.114 Angle : 0.520 12.946 30909 Z= 0.274 Chirality : 0.041 0.195 3574 Planarity : 0.004 0.048 3695 Dihedral : 15.819 129.551 3471 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.26 % Rotamer: Outliers : 3.21 % Allowed : 25.61 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.17), residues: 2570 helix: 1.70 (0.15), residues: 1243 sheet: 0.37 (0.22), residues: 545 loop : -0.20 (0.24), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 230 TYR 0.011 0.001 TYR A 235 PHE 0.012 0.001 PHE A 201 TRP 0.011 0.001 TRP D 324 HIS 0.006 0.001 HIS E 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (22689) covalent geometry : angle 0.51986 / 0.27 (30909) hydrogen bonds : bond 0.03475 / 2.23 ( 1209) hydrogen bonds : angle 4.23424 / 3.00 ( 3506) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7305.74 seconds wall clock time: 125 minutes 26.00 seconds (7526.00 seconds total)