Starting phenix.real_space_refine on Fri Aug 7 11:37:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fs3_29412/08_2026/8fs3_29412.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fs3_29412/08_2026/8fs3_29412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fs3_29412/08_2026/8fs3_29412.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fs3_29412/08_2026/8fs3_29412.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8fs3_29412/08_2026/8fs3_29412.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fs3_29412/08_2026/8fs3_29412.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fs3_29412/08_2026/8fs3_29412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fs3_29412/08_2026/8fs3_29412.map" } resolution = 2.93 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= 0.032 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 40 5.49 5 Mg 4 5.21 5 S 114 5.16 5 C 13358 2.51 5 N 3643 2.21 5 O 4063 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 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: 21222 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3564 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 419} 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: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2593 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 12, 'TRANS': 315} 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: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2732 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "F" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2240 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 9, 'TRANS': 268} Chain breaks: 7 Chain: "G" Number of atoms: 2257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2257 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 4, 'TRANS': 280} Chain breaks: 3 Chain: "H" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2017 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 8, 'TRANS': 240} Chain breaks: 6 Chain: "I" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 344 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain breaks: 1 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: 4.06, per 1000 atoms: 0.19 Number of scatterers: 21222 At special positions: 0 Unit cell: (111.78, 134.964, 137.448, 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 40 15.00 Mg 4 11.99 O 4063 8.00 N 3643 7.00 C 13358 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: 1.79 Conformation dependent library (CDL) restraints added in 700.9 milliseconds 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4920 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 14 sheets defined 53.5% alpha, 14.9% beta 10 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.560A pdb=" N VAL A 78 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 97 removed outlier: 3.665A pdb=" N ALA A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 126 removed outlier: 3.637A pdb=" N VAL A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 removed outlier: 3.651A pdb=" N TYR A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) 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 245 through 250 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 269 through 283 Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 292 through 295 removed outlier: 4.043A pdb=" N ASN A 295 " --> pdb=" O ASN A 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 292 through 295' Processing helix chain 'A' and resid 296 through 308 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: 3.976A 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: 3.517A pdb=" N ALA A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 432 removed outlier: 3.627A pdb=" N ASN A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 470 removed outlier: 3.890A pdb=" N TYR A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) 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 removed outlier: 3.515A pdb=" N ILE B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 69 through 72 removed outlier: 4.291A 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: 3.593A 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: 3.517A pdb=" N LYS B 149 " --> pdb=" O GLN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 156 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 removed outlier: 3.549A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 257 Processing helix chain 'B' and resid 262 through 276 removed outlier: 3.518A pdb=" N ASN B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 301 Processing helix chain 'B' and resid 305 through 321 removed outlier: 3.688A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 13 removed outlier: 3.540A pdb=" N ASN C 12 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU C 13 " --> pdb=" O LYS C 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 9 through 13' 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: 3.872A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.209A 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: 4.282A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.720A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 160 Processing helix chain 'C' and resid 170 through 186 removed outlier: 3.530A pdb=" N ILE C 174 " --> pdb=" O PRO C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.705A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.731A 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 253 Processing helix chain 'C' and resid 255 through 271 removed outlier: 4.011A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 3.922A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 313 Processing helix chain 'C' and resid 315 through 331 Processing helix chain 'C' and resid 331 through 336 removed outlier: 4.189A pdb=" N THR C 335 " --> pdb=" O PHE C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 42 through 55 removed outlier: 3.775A 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: 4.433A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.840A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.388A 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 142 through 145 Processing helix chain 'D' and resid 146 through 160 removed outlier: 4.497A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR D 160 " --> pdb=" O THR D 156 " (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: 5.249A pdb=" N ASP D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ARG D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 227 through 246 removed outlier: 3.699A pdb=" N GLY D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 260 Processing helix chain 'D' and resid 264 through 277 Processing helix chain 'D' and resid 279 through 293 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 removed outlier: 3.551A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 32 removed outlier: 4.637A 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 98 through 101 Processing helix chain 'E' and resid 102 through 103 No H-bonds generated for 'chain 'E' and resid 102 through 103' Processing helix chain 'E' and resid 104 through 119 removed outlier: 4.115A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 146 removed outlier: 3.531A pdb=" N LEU E 146 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 161 removed outlier: 3.512A pdb=" N ALA E 153 " --> pdb=" O ASP E 149 " (cutoff:3.500A) removed outlier: 4.099A 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 210 Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.506A pdb=" N LYS E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE E 222 " --> pdb=" O ILE E 218 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 243 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 308 Processing helix chain 'E' and resid 314 through 335 Processing helix chain 'E' and resid 337 through 354 removed outlier: 4.308A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP E 354 " --> pdb=" O MET E 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 30 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 112 removed outlier: 3.609A pdb=" N LEU F 100 " --> pdb=" O ASN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 219 removed outlier: 3.673A pdb=" N ARG F 219 " --> pdb=" O ALA F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 252 removed outlier: 4.550A pdb=" N SER F 244 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA F 245 " --> pdb=" O GLU F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 256 removed outlier: 3.999A pdb=" N TYR F 256 " --> pdb=" O VAL F 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 253 through 256' Processing helix chain 'F' and resid 412 through 424 removed outlier: 3.614A pdb=" N ALA F 424 " --> pdb=" O LYS F 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 28 removed outlier: 4.220A pdb=" N ILE G 21 " --> pdb=" O HIS G 17 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU G 28 " --> pdb=" O ALA G 24 " (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 174 Processing helix chain 'G' and resid 239 through 243 Processing helix chain 'G' and resid 245 through 252 removed outlier: 4.117A pdb=" N ILE G 251 " --> pdb=" O LYS G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 318 through 330 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: 3.902A 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: 5.920A pdb=" N THR A 149 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 109 through 114 removed outlier: 6.251A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY B 49 " --> pdb=" O CYS B 144 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TYR B 163 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER B 48 " --> pdb=" O TYR B 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.041A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.488A pdb=" N MET D 61 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N CYS D 170 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE D 63 " --> pdb=" O CYS D 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 69 through 76 removed outlier: 3.707A pdb=" N HIS E 93 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU E 40 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 212 through 213 removed outlier: 6.789A pdb=" N GLN E 212 " --> pdb=" O LEU E 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 82 through 83 removed outlier: 3.720A pdb=" N GLU F 94 " --> pdb=" O LYS F 210 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG F 41 " --> pdb=" O ASN F 38 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY F 462 " --> pdb=" O LEU F 444 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER F 437 " --> pdb=" O SER F 433 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU F 427 " --> pdb=" O SER F 443 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL F 428 " --> pdb=" O LEU F 235 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 408 through 411 removed outlier: 3.996A pdb=" N VAL F 267 " --> pdb=" O GLU F 280 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU F 280 " --> pdb=" O VAL F 267 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG G 129 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE G 121 " --> pdb=" O GLU G 128 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 80 through 85 removed outlier: 7.212A pdb=" N ASP G 36 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLU G 51 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL G 305 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE G 304 " --> pdb=" O SER G 271 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU G 270 " --> pdb=" O LYS G 254 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS G 254 " --> pdb=" O LEU G 270 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS G 216 " --> pdb=" O ILE G 157 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 233 through 238 removed outlier: 3.548A pdb=" N GLU G 177 " --> pdb=" O LYS G 197 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE G 192 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU H 139 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER H 115 " --> pdb=" O GLU H 139 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE H 116 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE H 3 " --> pdb=" O VAL H 120 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 152 through 153 removed outlier: 7.021A pdb=" N ASP H 29 " --> pdb=" O MET H 44 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N MET H 44 " --> pdb=" O ASP H 29 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE H 40 " --> pdb=" O THR H 33 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS H 52 " --> pdb=" O SER H 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 295 through 297 Processing sheet with id=AB4, first strand: chain 'H' and resid 284 through 289 removed outlier: 3.590A pdb=" N GLU H 251 " --> pdb=" O PHE H 266 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 270 through 271 removed outlier: 3.605A pdb=" N ARG H 279 " --> pdb=" O VAL H 270 " (cutoff:3.500A) 1132 hydrogen bonds defined for protein. 3267 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 4.25 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 6925 1.36 - 1.50: 5618 1.50 - 1.65: 8916 1.65 - 1.80: 81 1.80 - 1.95: 89 Bond restraints: 21629 Sorted by residual: bond pdb=" N LYS A 498 " pdb=" CA LYS A 498 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.18e-02 7.18e+03 1.26e+01 bond pdb=" C3' DA K 8 " pdb=" C2' DA K 8 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DC K 5 " pdb=" C2' DC K 5 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C LYS A 498 " pdb=" O LYS A 498 " ideal model delta sigma weight residual 1.236 1.277 -0.041 1.28e-02 6.10e+03 1.03e+01 bond pdb=" N ILE H 360 " pdb=" CA ILE H 360 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 1.00e+01 ... (remaining 21624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 28693 2.18 - 4.36: 583 4.36 - 6.54: 52 6.54 - 8.72: 4 8.72 - 10.90: 2 Bond angle restraints: 29334 Sorted by residual: angle pdb=" O4' DT I 29 " pdb=" C4' DT I 29 " pdb=" C3' DT I 29 " ideal model delta sigma weight residual 106.00 102.82 3.18 6.00e-01 2.78e+00 2.81e+01 angle pdb=" N GLU C 294 " pdb=" CA GLU C 294 " pdb=" C GLU C 294 " ideal model delta sigma weight residual 112.89 107.10 5.79 1.24e+00 6.50e-01 2.18e+01 angle pdb=" N3 DT I 13 " pdb=" C4 DT I 13 " pdb=" O4 DT I 13 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.08e+01 angle pdb=" O4' DC I 20 " pdb=" C4' DC I 20 " pdb=" C3' DC I 20 " ideal model delta sigma weight residual 106.00 103.29 2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" N3 DT K 7 " pdb=" C4 DT K 7 " pdb=" O4 DT K 7 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 ... (remaining 29329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.54: 12446 34.54 - 69.08: 654 69.08 - 103.62: 26 103.62 - 138.16: 2 138.16 - 172.69: 1 Dihedral angle restraints: 13129 sinusoidal: 5588 harmonic: 7541 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 300.00 127.31 172.69 1 2.00e+01 2.50e-03 4.78e+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 74.45 -134.45 1 2.00e+01 2.50e-03 4.08e+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 56.94 -116.95 1 2.00e+01 2.50e-03 3.49e+01 ... (remaining 13126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2961 0.068 - 0.136: 415 0.136 - 0.204: 24 0.204 - 0.272: 2 0.272 - 0.340: 1 Chirality restraints: 3403 Sorted by residual: chirality pdb=" CB THR D 47 " pdb=" CA THR D 47 " pdb=" OG1 THR D 47 " pdb=" CG2 THR D 47 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CB ILE B 47 " pdb=" CA ILE B 47 " pdb=" CG1 ILE B 47 " pdb=" CG2 ILE B 47 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.43e+00 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 2.65 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 3400 not shown) Planarity restraints: 3593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 213 " 0.026 2.00e-02 2.50e+03 2.78e-02 1.35e+01 pdb=" CG PHE F 213 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE F 213 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE F 213 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE F 213 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE F 213 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE F 213 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 294 " 0.020 2.00e-02 2.50e+03 2.30e-02 1.32e+01 pdb=" CG TRP A 294 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP A 294 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP A 294 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 294 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP A 294 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 294 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 294 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 294 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 294 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 180 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C LYS B 180 " 0.057 2.00e-02 2.50e+03 pdb=" O LYS B 180 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU B 181 " -0.019 2.00e-02 2.50e+03 ... (remaining 3590 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 154 2.51 - 3.11: 15292 3.11 - 3.70: 33162 3.70 - 4.30: 48382 4.30 - 4.90: 81164 Nonbonded interactions: 178154 Sorted by model distance: nonbonded pdb="MG MG A 601 " pdb=" O3A AGS A 602 " model vdw 1.912 2.170 nonbonded pdb="MG MG C 401 " pdb=" O2G AGS C 402 " model vdw 1.943 2.170 nonbonded pdb=" OG1 THR B 56 " pdb="MG MG B 402 " model vdw 1.965 2.170 nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 1.966 2.170 nonbonded pdb=" OG SER A 116 " pdb="MG MG A 601 " model vdw 1.983 2.170 ... (remaining 178149 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: 5.330 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: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 20.490 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21629 Z= 0.261 Angle : 0.687 10.904 29334 Z= 0.426 Chirality : 0.046 0.340 3403 Planarity : 0.005 0.095 3593 Dihedral : 18.385 172.694 8209 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.30 % Allowed : 27.80 % Favored : 67.90 % 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: 0.21 (0.17), residues: 2518 helix: 0.91 (0.15), residues: 1238 sheet: -0.12 (0.24), residues: 516 loop : -0.76 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 136 TYR 0.026 0.002 TYR B 163 PHE 0.065 0.002 PHE F 213 TRP 0.059 0.002 TRP A 294 HIS 0.014 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.26 (21629) covalent geometry : angle 0.68652 / 0.43 (29334) hydrogen bonds : bond 0.17428 / 11.49 ( 1156) hydrogen bonds : angle 7.05804 / 5.00 ( 3315) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 280 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: A 273 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7099 (mp) REVERT: C 136 ARG cc_start: 0.7588 (ttt90) cc_final: 0.7380 (ttt90) REVERT: F 436 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7095 (tp30) REVERT: G 60 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7066 (tp) outliers start: 100 outliers final: 77 residues processed: 363 average time/residue: 0.4991 time to fit residues: 212.7234 Evaluate side-chains 338 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 258 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 PHE 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 204 LEU Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 18 HIS Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 221 ARG Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 286 ASN Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 190 ASN Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 258 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.6980 chunk 247 optimal weight: 9.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 HIS A 284 ASN B 102 HIS C 30 GLN D 24 GLN D 207 GLN D 311 ASN E 104 ASN F 291 HIS H 45 ASN H 355 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.199855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.151671 restraints weight = 23761.280| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.35 r_work: 0.3494 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21629 Z= 0.216 Angle : 0.656 11.036 29334 Z= 0.343 Chirality : 0.045 0.173 3403 Planarity : 0.005 0.053 3593 Dihedral : 14.017 147.725 3211 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 6.88 % Allowed : 24.70 % Favored : 68.42 % 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: 0.24 (0.17), residues: 2518 helix: 0.91 (0.15), residues: 1238 sheet: -0.15 (0.23), residues: 533 loop : -0.69 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 136 TYR 0.023 0.002 TYR A 497 PHE 0.026 0.002 PHE G 40 TRP 0.014 0.002 TRP D 324 HIS 0.012 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 (21629) covalent geometry : angle 0.65551 / 0.34 (29334) hydrogen bonds : bond 0.05463 / 3.61 ( 1156) hydrogen bonds : angle 5.53449 / 3.89 ( 3315) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 287 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6754 (tm-30) REVERT: A 119 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7555 (mp) REVERT: A 256 MET cc_start: 0.6381 (mpt) cc_final: 0.6120 (mpm) REVERT: A 273 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7258 (mp) REVERT: A 465 ASN cc_start: 0.6493 (t0) cc_final: 0.6109 (m-40) REVERT: B 39 ASP cc_start: 0.7949 (m-30) cc_final: 0.7743 (m-30) REVERT: C 66 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8091 (tp) REVERT: C 99 ASP cc_start: 0.8154 (m-30) cc_final: 0.7944 (m-30) REVERT: C 204 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8034 (t0) REVERT: D 80 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7595 (ttpt) REVERT: D 86 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7190 (m-30) REVERT: D 148 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7762 (m-30) REVERT: D 190 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.7178 (mmtp) REVERT: D 254 THR cc_start: 0.8386 (m) cc_final: 0.8099 (m) REVERT: E 18 HIS cc_start: 0.8508 (OUTLIER) cc_final: 0.7351 (p-80) REVERT: E 52 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.5175 (mtt90) REVERT: E 119 MET cc_start: 0.7661 (ttp) cc_final: 0.7423 (ttp) REVERT: E 184 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8331 (mtm180) REVERT: E 220 LYS cc_start: 0.7363 (mppt) cc_final: 0.7015 (mppt) REVERT: F 94 GLU cc_start: 0.4507 (OUTLIER) cc_final: 0.4132 (tm-30) REVERT: F 265 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7080 (tmm) REVERT: F 436 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7000 (tp30) REVERT: G 60 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7266 (tp) REVERT: H 20 ILE cc_start: 0.6027 (mm) cc_final: 0.5644 (mt) outliers start: 160 outliers final: 64 residues processed: 405 average time/residue: 0.5287 time to fit residues: 247.7303 Evaluate side-chains 346 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 266 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 204 ASP 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 80 LYS Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 18 HIS Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 184 ARG Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 265 MET Chi-restraints excluded: chain F residue 286 ASN Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 407 GLU Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain F residue 440 PHE Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 147 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 82 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 208 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 GLN B 146 GLN D 24 GLN D 207 GLN D 352 GLN E 104 ASN F 291 HIS G 268 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.200451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.150122 restraints weight = 23732.363| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.00 r_work: 0.3523 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21629 Z= 0.180 Angle : 0.613 10.952 29334 Z= 0.318 Chirality : 0.043 0.171 3403 Planarity : 0.004 0.047 3593 Dihedral : 13.584 137.788 3148 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 6.07 % Allowed : 25.82 % Favored : 68.12 % 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: 0.35 (0.17), residues: 2518 helix: 1.02 (0.15), residues: 1234 sheet: -0.09 (0.23), residues: 535 loop : -0.68 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 136 TYR 0.016 0.001 TYR A 497 PHE 0.019 0.002 PHE H 240 TRP 0.014 0.001 TRP D 324 HIS 0.011 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (21629) covalent geometry : angle 0.61257 / 0.32 (29334) hydrogen bonds : bond 0.04850 / 3.20 ( 1156) hydrogen bonds : angle 5.23625 / 3.67 ( 3315) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 277 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6710 (tm-30) REVERT: A 119 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7515 (mp) REVERT: A 273 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7217 (mp) REVERT: A 285 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7380 (tpp) REVERT: A 465 ASN cc_start: 0.6552 (t0) cc_final: 0.6152 (m-40) REVERT: C 66 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8106 (tp) REVERT: C 204 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8082 (m-30) REVERT: D 80 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7570 (ttpt) REVERT: D 86 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7207 (m-30) REVERT: D 190 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.7154 (mmtp) REVERT: D 254 THR cc_start: 0.8418 (m) cc_final: 0.8155 (m) REVERT: E 52 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.5136 (mtt90) REVERT: E 119 MET cc_start: 0.7751 (ttp) cc_final: 0.7537 (ttp) REVERT: E 184 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8316 (mtm180) REVERT: F 265 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.6994 (tmm) REVERT: F 436 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7018 (tp30) REVERT: G 60 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7301 (tp) REVERT: G 155 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6695 (pp20) REVERT: G 218 GLN cc_start: 0.6821 (mt0) cc_final: 0.5899 (mm-40) REVERT: G 238 ASP cc_start: 0.7117 (t0) cc_final: 0.6699 (t0) REVERT: H 20 ILE cc_start: 0.6081 (mm) cc_final: 0.5690 (mt) outliers start: 141 outliers final: 76 residues processed: 382 average time/residue: 0.4948 time to fit residues: 220.1545 Evaluate side-chains 350 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 259 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 250 SER 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 80 LYS Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 184 ARG Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 265 MET Chi-restraints excluded: chain F residue 286 ASN Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 407 GLU Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain F residue 440 PHE Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 254 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 129 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 chunk 175 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 166 optimal weight: 0.6980 chunk 170 optimal weight: 0.9990 chunk 218 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 GLN D 24 GLN D 207 GLN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN F 291 HIS H 97 ASN H 233 ASN H 259 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.202035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.152534 restraints weight = 23801.021| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.09 r_work: 0.3537 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21629 Z= 0.134 Angle : 0.569 10.316 29334 Z= 0.297 Chirality : 0.042 0.214 3403 Planarity : 0.004 0.045 3593 Dihedral : 13.393 125.743 3139 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 5.98 % Allowed : 25.43 % Favored : 68.59 % 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: 0.56 (0.17), residues: 2518 helix: 1.21 (0.15), residues: 1238 sheet: -0.05 (0.23), residues: 531 loop : -0.55 (0.24), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 136 TYR 0.016 0.001 TYR G 181 PHE 0.017 0.001 PHE G 202 TRP 0.013 0.001 TRP D 324 HIS 0.012 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (21629) covalent geometry : angle 0.56896 / 0.30 (29334) hydrogen bonds : bond 0.04137 / 2.73 ( 1156) hydrogen bonds : angle 4.97301 / 3.47 ( 3315) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 289 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.6742 (tm-30) REVERT: A 163 MET cc_start: 0.6341 (OUTLIER) cc_final: 0.5800 (mtm) REVERT: A 288 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6472 (mm) REVERT: A 465 ASN cc_start: 0.6507 (t0) cc_final: 0.6110 (m-40) REVERT: C 81 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8362 (tt0) REVERT: C 204 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8054 (m-30) REVERT: D 86 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.7172 (m-30) REVERT: D 249 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8537 (ttpt) REVERT: D 254 THR cc_start: 0.8337 (m) cc_final: 0.8086 (m) REVERT: D 258 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7674 (pt0) REVERT: E 52 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.5208 (mtt90) REVERT: E 119 MET cc_start: 0.7712 (ttp) cc_final: 0.7495 (ttp) REVERT: E 184 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8211 (mtm180) REVERT: F 87 GLU cc_start: 0.4977 (OUTLIER) cc_final: 0.4441 (pm20) REVERT: G 66 LEU cc_start: 0.7597 (tt) cc_final: 0.7196 (mp) REVERT: G 95 VAL cc_start: 0.3064 (OUTLIER) cc_final: 0.2758 (p) REVERT: G 155 GLU cc_start: 0.7083 (tt0) cc_final: 0.6621 (pp20) REVERT: G 218 GLN cc_start: 0.6883 (mt0) cc_final: 0.5933 (mm-40) REVERT: G 238 ASP cc_start: 0.7056 (t0) cc_final: 0.6356 (t0) REVERT: H 20 ILE cc_start: 0.6020 (mm) cc_final: 0.5644 (mt) REVERT: H 370 LYS cc_start: 0.6061 (tmtt) cc_final: 0.5822 (tmtt) outliers start: 139 outliers final: 70 residues processed: 392 average time/residue: 0.5282 time to fit residues: 240.8559 Evaluate side-chains 349 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 268 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 220 ASP 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 88 MET Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 184 ARG Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 286 ASN Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 407 GLU Chi-restraints excluded: chain F residue 440 PHE Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 254 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 16 optimal weight: 0.7980 chunk 203 optimal weight: 0.9990 chunk 220 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 199 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 GLN B 8 GLN C 95 ASN D 24 GLN E 18 HIS E 104 ASN F 291 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.202162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.152538 restraints weight = 23601.182| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.97 r_work: 0.3547 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21629 Z= 0.142 Angle : 0.570 10.477 29334 Z= 0.295 Chirality : 0.042 0.158 3403 Planarity : 0.004 0.044 3593 Dihedral : 13.224 121.779 3130 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 6.24 % Allowed : 25.56 % Favored : 68.20 % 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: 0.63 (0.17), residues: 2518 helix: 1.26 (0.15), residues: 1240 sheet: -0.04 (0.23), residues: 530 loop : -0.50 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 136 TYR 0.017 0.001 TYR B 186 PHE 0.024 0.001 PHE A 279 TRP 0.013 0.001 TRP D 324 HIS 0.011 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (21629) covalent geometry : angle 0.57014 / 0.30 (29334) hydrogen bonds : bond 0.04128 / 2.72 ( 1156) hydrogen bonds : angle 4.87306 / 3.40 ( 3315) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 273 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6726 (tm-30) REVERT: A 163 MET cc_start: 0.6361 (OUTLIER) cc_final: 0.5840 (mtm) REVERT: A 285 MET cc_start: 0.8078 (ttp) cc_final: 0.7579 (tpp) REVERT: A 288 LEU cc_start: 0.6836 (OUTLIER) cc_final: 0.6551 (mm) REVERT: A 465 ASN cc_start: 0.6618 (t0) cc_final: 0.6188 (m-40) REVERT: C 104 ARG cc_start: 0.8189 (ttm170) cc_final: 0.7975 (ttm170) REVERT: C 204 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.8062 (m-30) REVERT: D 80 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7491 (ttpt) REVERT: D 86 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.7051 (m-30) REVERT: D 148 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7666 (p0) REVERT: D 190 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.7679 (mttp) REVERT: D 254 THR cc_start: 0.8293 (m) cc_final: 0.8049 (m) REVERT: D 259 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8518 (pt) REVERT: E 18 HIS cc_start: 0.8299 (OUTLIER) cc_final: 0.7732 (p-80) REVERT: E 52 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.5206 (mtt90) REVERT: E 119 MET cc_start: 0.7761 (ttp) cc_final: 0.7538 (ttp) REVERT: E 184 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8210 (mtm180) REVERT: F 87 GLU cc_start: 0.5169 (OUTLIER) cc_final: 0.4569 (pm20) REVERT: G 95 VAL cc_start: 0.3084 (OUTLIER) cc_final: 0.2781 (p) REVERT: G 154 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7497 (p90) REVERT: G 218 GLN cc_start: 0.6876 (mt0) cc_final: 0.6026 (mm-40) REVERT: G 238 ASP cc_start: 0.7137 (t0) cc_final: 0.6454 (t0) REVERT: H 20 ILE cc_start: 0.6076 (mm) cc_final: 0.5704 (mt) outliers start: 145 outliers final: 78 residues processed: 387 average time/residue: 0.4759 time to fit residues: 214.9802 Evaluate side-chains 352 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 259 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 117 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 220 ASP 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 80 LYS Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain E residue 18 HIS Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 184 ARG Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 286 ASN Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 407 GLU Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 440 PHE Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 254 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 12 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 163 optimal weight: 0.7980 chunk 237 optimal weight: 9.9990 chunk 247 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 chunk 176 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 GLN D 24 GLN D 207 GLN E 104 ASN F 291 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.201619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.151623 restraints weight = 23729.548| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.01 r_work: 0.3535 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21629 Z= 0.158 Angle : 0.583 10.322 29334 Z= 0.301 Chirality : 0.042 0.184 3403 Planarity : 0.004 0.044 3593 Dihedral : 13.172 120.219 3123 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 6.20 % Allowed : 25.47 % Favored : 68.33 % 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: 0.60 (0.17), residues: 2518 helix: 1.21 (0.15), residues: 1244 sheet: -0.02 (0.23), residues: 531 loop : -0.49 (0.24), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 136 TYR 0.018 0.001 TYR B 186 PHE 0.015 0.001 PHE G 40 TRP 0.013 0.001 TRP D 324 HIS 0.020 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (21629) covalent geometry : angle 0.58295 / 0.30 (29334) hydrogen bonds : bond 0.04195 / 2.76 ( 1156) hydrogen bonds : angle 4.82462 / 3.36 ( 3315) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 275 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.6718 (tm-30) REVERT: A 163 MET cc_start: 0.6313 (OUTLIER) cc_final: 0.5415 (mtm) REVERT: A 196 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7179 (t0) REVERT: A 256 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.6354 (mpm) REVERT: A 273 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7241 (mp) REVERT: A 285 MET cc_start: 0.8108 (ttp) cc_final: 0.7505 (tpp) REVERT: A 288 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6475 (mm) REVERT: A 294 TRP cc_start: 0.7452 (t-100) cc_final: 0.7114 (t-100) REVERT: B 87 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7451 (t0) REVERT: C 11 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6940 (tp30) REVERT: C 104 ARG cc_start: 0.8194 (ttm170) cc_final: 0.7809 (ttm170) REVERT: C 152 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8072 (mtpp) REVERT: C 204 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8081 (m-30) REVERT: C 292 ASN cc_start: 0.8496 (t0) cc_final: 0.8012 (t0) REVERT: D 80 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7543 (ttpt) REVERT: D 86 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.7053 (m-30) REVERT: D 190 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.7722 (mttp) REVERT: D 254 THR cc_start: 0.8324 (m) cc_final: 0.8057 (m) REVERT: D 258 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7616 (pt0) REVERT: E 8 TYR cc_start: 0.8730 (m-80) cc_final: 0.8480 (m-80) REVERT: E 220 LYS cc_start: 0.7375 (mppt) cc_final: 0.7096 (mppt) REVERT: F 87 GLU cc_start: 0.5129 (OUTLIER) cc_final: 0.4532 (pm20) REVERT: G 155 GLU cc_start: 0.7081 (tt0) cc_final: 0.6756 (pp20) REVERT: G 218 GLN cc_start: 0.6923 (mt0) cc_final: 0.5978 (mm-40) REVERT: G 238 ASP cc_start: 0.7114 (t0) cc_final: 0.6398 (t0) REVERT: H 20 ILE cc_start: 0.6076 (mm) cc_final: 0.5696 (mt) outliers start: 144 outliers final: 88 residues processed: 386 average time/residue: 0.5160 time to fit residues: 231.0132 Evaluate side-chains 365 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 263 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 117 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 250 SER 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 80 LYS Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 286 ASN Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 440 PHE Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 254 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 178 optimal weight: 0.6980 chunk 122 optimal weight: 0.3980 chunk 118 optimal weight: 0.9990 chunk 115 optimal weight: 0.0980 chunk 35 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 233 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 201 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 GLN D 24 GLN D 207 GLN E 104 ASN F 291 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.203118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.153361 restraints weight = 23663.927| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.02 r_work: 0.3556 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21629 Z= 0.124 Angle : 0.567 15.447 29334 Z= 0.292 Chirality : 0.041 0.156 3403 Planarity : 0.004 0.040 3593 Dihedral : 13.099 116.873 3123 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 5.38 % Allowed : 26.51 % Favored : 68.12 % 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: 0.72 (0.17), residues: 2518 helix: 1.31 (0.15), residues: 1242 sheet: 0.01 (0.23), residues: 531 loop : -0.43 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 20 TYR 0.018 0.001 TYR B 186 PHE 0.026 0.001 PHE A 279 TRP 0.012 0.001 TRP D 324 HIS 0.009 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (21629) covalent geometry : angle 0.56733 / 0.29 (29334) hydrogen bonds : bond 0.03834 / 2.53 ( 1156) hydrogen bonds : angle 4.73434 / 3.30 ( 3315) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 272 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.6721 (tm-30) REVERT: A 163 MET cc_start: 0.6326 (OUTLIER) cc_final: 0.5792 (mtm) REVERT: A 178 MET cc_start: 0.1558 (mmt) cc_final: 0.0306 (ttm) REVERT: A 273 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7193 (mp) REVERT: A 285 MET cc_start: 0.8115 (ttp) cc_final: 0.7506 (tpp) REVERT: A 288 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6544 (mm) REVERT: A 294 TRP cc_start: 0.7451 (t-100) cc_final: 0.7144 (t-100) REVERT: C 152 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.8050 (mtpp) REVERT: C 204 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.8002 (m-30) REVERT: C 292 ASN cc_start: 0.8507 (t0) cc_final: 0.8052 (t0) REVERT: D 86 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.7036 (m-30) REVERT: D 148 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7686 (p0) REVERT: D 190 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.7647 (mttp) REVERT: D 254 THR cc_start: 0.8325 (m) cc_final: 0.8101 (m) REVERT: E 8 TYR cc_start: 0.8769 (m-80) cc_final: 0.8546 (m-80) REVERT: F 87 GLU cc_start: 0.5153 (OUTLIER) cc_final: 0.4424 (pm20) REVERT: F 94 GLU cc_start: 0.4136 (OUTLIER) cc_final: 0.3790 (tm-30) REVERT: G 155 GLU cc_start: 0.7021 (tt0) cc_final: 0.6594 (pp20) REVERT: G 218 GLN cc_start: 0.6922 (mt0) cc_final: 0.5924 (mm-40) REVERT: G 238 ASP cc_start: 0.7117 (t0) cc_final: 0.6389 (t0) REVERT: H 20 ILE cc_start: 0.6056 (mm) cc_final: 0.5670 (mt) outliers start: 125 outliers final: 72 residues processed: 370 average time/residue: 0.4881 time to fit residues: 211.2704 Evaluate side-chains 344 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 261 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 117 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 220 ASP 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 94 GLU Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 286 ASN Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 407 GLU Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 440 PHE Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 254 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 34 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 218 optimal weight: 0.4980 chunk 78 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 GLN D 24 GLN E 104 ASN F 291 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.203620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.154732 restraints weight = 23614.737| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.99 r_work: 0.3567 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21629 Z= 0.126 Angle : 0.568 11.859 29334 Z= 0.291 Chirality : 0.041 0.170 3403 Planarity : 0.004 0.048 3593 Dihedral : 13.000 115.341 3120 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.69 % Allowed : 27.62 % Favored : 67.69 % 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: 0.77 (0.17), residues: 2518 helix: 1.35 (0.15), residues: 1242 sheet: 0.05 (0.23), residues: 539 loop : -0.40 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 136 TYR 0.019 0.001 TYR B 186 PHE 0.017 0.001 PHE G 154 TRP 0.013 0.001 TRP D 324 HIS 0.009 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (21629) covalent geometry : angle 0.56829 / 0.29 (29334) hydrogen bonds : bond 0.03797 / 2.50 ( 1156) hydrogen bonds : angle 4.66840 / 3.25 ( 3315) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 273 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.6651 (tm-30) REVERT: A 163 MET cc_start: 0.6315 (OUTLIER) cc_final: 0.5790 (mtm) REVERT: A 178 MET cc_start: 0.1553 (mmt) cc_final: 0.0307 (ttm) REVERT: A 273 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7243 (mp) REVERT: A 288 LEU cc_start: 0.6543 (OUTLIER) cc_final: 0.6275 (mm) REVERT: B 87 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7427 (t0) REVERT: C 204 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.8021 (m-30) REVERT: C 292 ASN cc_start: 0.8554 (t0) cc_final: 0.8108 (t0) REVERT: D 86 ASP cc_start: 0.7389 (OUTLIER) cc_final: 0.7017 (m-30) REVERT: D 190 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.7641 (mttp) REVERT: D 254 THR cc_start: 0.8283 (m) cc_final: 0.8039 (m) REVERT: E 8 TYR cc_start: 0.8771 (m-80) cc_final: 0.8504 (m-80) REVERT: F 231 MET cc_start: 0.5587 (mtp) cc_final: 0.5386 (ptm) REVERT: G 21 ILE cc_start: 0.7589 (mp) cc_final: 0.7181 (mp) REVERT: G 155 GLU cc_start: 0.7053 (tt0) cc_final: 0.6600 (pp20) REVERT: G 218 GLN cc_start: 0.6853 (mt0) cc_final: 0.5870 (mm-40) REVERT: G 238 ASP cc_start: 0.7052 (t0) cc_final: 0.6346 (t0) REVERT: H 20 ILE cc_start: 0.6097 (mm) cc_final: 0.5718 (mt) outliers start: 109 outliers final: 70 residues processed: 356 average time/residue: 0.4639 time to fit residues: 192.8729 Evaluate side-chains 332 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 254 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 117 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 220 ASP 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 94 GLU Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 286 ASN Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 407 GLU Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 440 PHE Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 147 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 216 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 106 optimal weight: 0.0570 chunk 32 optimal weight: 0.8980 chunk 209 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 192 optimal weight: 6.9990 overall best weight: 1.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 GLN D 24 GLN E 18 HIS E 104 ASN E 292 HIS F 291 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.199903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.149462 restraints weight = 23786.694| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.03 r_work: 0.3509 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 21629 Z= 0.200 Angle : 0.633 12.383 29334 Z= 0.325 Chirality : 0.044 0.177 3403 Planarity : 0.004 0.064 3593 Dihedral : 13.108 115.049 3118 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.69 % Allowed : 27.93 % Favored : 67.38 % 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: 0.54 (0.17), residues: 2518 helix: 1.11 (0.15), residues: 1247 sheet: -0.01 (0.23), residues: 540 loop : -0.49 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 136 TYR 0.019 0.002 TYR B 186 PHE 0.035 0.002 PHE A 279 TRP 0.023 0.002 TRP A 294 HIS 0.008 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 (21629) covalent geometry : angle 0.63274 / 0.32 (29334) hydrogen bonds : bond 0.04556 / 3.01 ( 1156) hydrogen bonds : angle 4.81862 / 3.36 ( 3315) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 267 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6596 (tm-30) REVERT: A 163 MET cc_start: 0.6314 (OUTLIER) cc_final: 0.5775 (mtm) REVERT: A 273 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7376 (mp) REVERT: A 288 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6234 (mm) REVERT: B 87 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7470 (t0) REVERT: C 11 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6942 (tp30) REVERT: C 66 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8080 (tp) REVERT: C 204 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8118 (m-30) REVERT: C 292 ASN cc_start: 0.8586 (t0) cc_final: 0.8067 (t0) REVERT: D 80 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7575 (ttpt) REVERT: D 86 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7066 (m-30) REVERT: D 190 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.7804 (mttp) REVERT: D 254 THR cc_start: 0.8376 (m) cc_final: 0.8091 (m) REVERT: E 8 TYR cc_start: 0.8774 (m-80) cc_final: 0.8452 (m-80) REVERT: E 158 MET cc_start: 0.8822 (ptt) cc_final: 0.8594 (ptt) REVERT: E 220 LYS cc_start: 0.7368 (mppt) cc_final: 0.7043 (mppt) REVERT: F 231 MET cc_start: 0.5646 (mtp) cc_final: 0.5395 (ptm) REVERT: G 21 ILE cc_start: 0.7639 (mp) cc_final: 0.7221 (mp) REVERT: G 60 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7246 (tp) REVERT: G 155 GLU cc_start: 0.7128 (tt0) cc_final: 0.6729 (pp20) REVERT: G 218 GLN cc_start: 0.6932 (mt0) cc_final: 0.6011 (mm-40) REVERT: G 238 ASP cc_start: 0.7153 (t0) cc_final: 0.6540 (t0) REVERT: G 323 GLU cc_start: 0.6757 (tp30) cc_final: 0.5980 (mt-10) REVERT: H 20 ILE cc_start: 0.6117 (mm) cc_final: 0.5727 (mt) outliers start: 109 outliers final: 73 residues processed: 352 average time/residue: 0.4968 time to fit residues: 204.1757 Evaluate side-chains 342 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 257 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 117 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 220 ASP 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 80 LYS Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 286 ASN Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 440 PHE Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 254 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 222 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 240 optimal weight: 1.9990 chunk 230 optimal weight: 0.8980 chunk 224 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 33 optimal weight: 0.2980 chunk 91 optimal weight: 0.8980 chunk 251 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 GLN D 24 GLN E 104 ASN F 291 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.202072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.152410 restraints weight = 23758.857| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.06 r_work: 0.3540 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21629 Z= 0.137 Angle : 0.591 11.194 29334 Z= 0.304 Chirality : 0.042 0.160 3403 Planarity : 0.004 0.049 3593 Dihedral : 13.064 116.504 3118 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.87 % Allowed : 28.87 % Favored : 67.25 % 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: 0.64 (0.17), residues: 2518 helix: 1.21 (0.15), residues: 1250 sheet: -0.00 (0.23), residues: 540 loop : -0.43 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 136 TYR 0.025 0.001 TYR C 71 PHE 0.026 0.001 PHE H 332 TRP 0.020 0.001 TRP A 294 HIS 0.006 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (21629) covalent geometry : angle 0.59140 / 0.30 (29334) hydrogen bonds : bond 0.03937 / 2.60 ( 1156) hydrogen bonds : angle 4.73363 / 3.30 ( 3315) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 259 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.6615 (tm-30) REVERT: A 163 MET cc_start: 0.6307 (OUTLIER) cc_final: 0.5783 (mtm) REVERT: A 273 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7357 (mp) REVERT: A 288 LEU cc_start: 0.6623 (OUTLIER) cc_final: 0.6421 (mm) REVERT: C 204 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8074 (m-30) REVERT: C 292 ASN cc_start: 0.8608 (t0) cc_final: 0.8124 (t0) REVERT: D 86 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.7018 (m-30) REVERT: D 190 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.7679 (mttp) REVERT: D 254 THR cc_start: 0.8300 (m) cc_final: 0.8038 (m) REVERT: G 21 ILE cc_start: 0.7583 (mp) cc_final: 0.7154 (mp) REVERT: G 155 GLU cc_start: 0.7091 (tt0) cc_final: 0.6734 (pp20) REVERT: G 218 GLN cc_start: 0.6886 (mt0) cc_final: 0.5988 (mm-40) REVERT: G 238 ASP cc_start: 0.7090 (t0) cc_final: 0.6311 (t0) REVERT: G 323 GLU cc_start: 0.6715 (tp30) cc_final: 0.5984 (mt-10) REVERT: H 7 ILE cc_start: 0.5928 (pt) cc_final: 0.5695 (pt) REVERT: H 20 ILE cc_start: 0.6108 (mm) cc_final: 0.5723 (mt) REVERT: H 35 THR cc_start: 0.6998 (m) cc_final: 0.6542 (p) outliers start: 90 outliers final: 67 residues processed: 333 average time/residue: 0.5015 time to fit residues: 195.2838 Evaluate side-chains 325 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 251 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 117 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 220 ASP 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 94 GLU Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 286 ASN Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 440 PHE Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 254 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 172 optimal weight: 0.8980 chunk 74 optimal weight: 0.0040 chunk 5 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 221 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 GLN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN E 104 ASN F 291 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.202758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.153962 restraints weight = 23691.537| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.04 r_work: 0.3555 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21629 Z= 0.128 Angle : 0.585 10.899 29334 Z= 0.301 Chirality : 0.042 0.152 3403 Planarity : 0.004 0.040 3593 Dihedral : 12.990 115.955 3118 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.92 % Allowed : 28.96 % Favored : 67.13 % 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: 0.72 (0.17), residues: 2518 helix: 1.29 (0.15), residues: 1244 sheet: 0.05 (0.23), residues: 541 loop : -0.41 (0.24), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG F 20 TYR 0.026 0.001 TYR C 71 PHE 0.036 0.001 PHE H 332 TRP 0.024 0.001 TRP A 294 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (21629) covalent geometry : angle 0.58523 / 0.30 (29334) hydrogen bonds : bond 0.03804 / 2.52 ( 1156) hydrogen bonds : angle 4.68984 / 3.27 ( 3315) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7848.81 seconds wall clock time: 134 minutes 32.52 seconds (8072.52 seconds total)