Starting phenix.real_space_refine on Sun Aug 24 23:05:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dvi_27739/08_2025/8dvi_27739.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dvi_27739/08_2025/8dvi_27739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dvi_27739/08_2025/8dvi_27739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dvi_27739/08_2025/8dvi_27739.map" model { file = "/net/cci-nas-00/data/ceres_data/8dvi_27739/08_2025/8dvi_27739.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dvi_27739/08_2025/8dvi_27739.cif" } resolution = 3.2 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= 0.004 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 32 5.49 5 Mg 5 5.21 5 S 132 5.16 5 C 14995 2.51 5 N 3943 2.21 5 O 4586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23693 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "B" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "C" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "D" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "E" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "F" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "M" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "H" Number of atoms: 2644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2644 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain breaks: 1 Chain: "T" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} 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: 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: "F" 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} Time building chain proxies: 5.09, per 1000 atoms: 0.21 Number of scatterers: 23693 At special positions: 0 Unit cell: (134.136, 130.824, 142.416, 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 132 16.00 P 32 15.00 Mg 5 11.99 O 4586 8.00 N 3943 7.00 C 14995 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: 1.92 Conformation dependent library (CDL) restraints added in 796.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5530 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 20 sheets defined 53.8% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 Processing helix chain 'A' and resid 13 through 20 Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 24 through 28 Processing helix chain 'A' and resid 31 through 47 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 66 through 79 Processing helix chain 'A' and resid 86 through 118 Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 176 through 183 Processing helix chain 'A' and resid 202 through 217 removed outlier: 4.527A pdb=" N GLY A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 243 Processing helix chain 'A' and resid 245 through 252 removed outlier: 3.520A pdb=" N ILE A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 269 removed outlier: 3.550A pdb=" N LYS A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 301 Processing helix chain 'A' and resid 328 through 347 Processing helix chain 'A' and resid 357 through 363 Processing helix chain 'A' and resid 390 through 396 Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'B' and resid 12 through 20 Processing helix chain 'B' and resid 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 24 through 28 removed outlier: 3.542A pdb=" N TYR B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE B 28 " --> pdb=" O SER B 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 24 through 28' Processing helix chain 'B' and resid 31 through 48 Processing helix chain 'B' and resid 52 through 58 Processing helix chain 'B' and resid 66 through 80 Processing helix chain 'B' and resid 88 through 119 removed outlier: 3.529A pdb=" N LEU B 119 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 133 Processing helix chain 'B' and resid 134 through 143 Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 176 through 184 removed outlier: 3.512A pdb=" N ILE B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 217 Processing helix chain 'B' and resid 229 through 243 removed outlier: 3.568A pdb=" N ASP B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 Processing helix chain 'B' and resid 255 through 269 removed outlier: 3.842A pdb=" N LYS B 269 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 301 Processing helix chain 'B' and resid 327 through 347 removed outlier: 3.589A pdb=" N THR B 331 " --> pdb=" O ASN B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'B' and resid 391 through 396 removed outlier: 3.628A pdb=" N ALA B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 13 through 20 Processing helix chain 'C' and resid 24 through 28 removed outlier: 3.769A pdb=" N PHE C 28 " --> pdb=" O SER C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 47 Processing helix chain 'C' and resid 52 through 63 Processing helix chain 'C' and resid 66 through 77 removed outlier: 4.001A pdb=" N GLY C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 119 Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 133 through 143 Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 203 through 217 Processing helix chain 'C' and resid 229 through 242 Processing helix chain 'C' and resid 245 through 252 Processing helix chain 'C' and resid 255 through 268 Processing helix chain 'C' and resid 286 through 301 Processing helix chain 'C' and resid 312 through 316 removed outlier: 3.640A pdb=" N ILE C 315 " --> pdb=" O TYR C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 347 Processing helix chain 'C' and resid 357 through 361 removed outlier: 3.653A pdb=" N TRP C 361 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 375 through 381 removed outlier: 3.957A pdb=" N ALA C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 395 Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 12 through 20 removed outlier: 3.607A pdb=" N LYS D 18 " --> pdb=" O ALA D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 23 No H-bonds generated for 'chain 'D' and resid 21 through 23' Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.502A pdb=" N TYR D 27 " --> pdb=" O ASP D 24 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE D 28 " --> pdb=" O SER D 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 24 through 28' Processing helix chain 'D' and resid 31 through 48 removed outlier: 3.671A pdb=" N PHE D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 62 Processing helix chain 'D' and resid 66 through 80 Processing helix chain 'D' and resid 86 through 118 Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 133 through 143 removed outlier: 3.936A pdb=" N ILE D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 163 Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 204 through 217 Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'D' and resid 245 through 252 Processing helix chain 'D' and resid 255 through 268 Processing helix chain 'D' and resid 286 through 301 Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 327 through 347 Processing helix chain 'D' and resid 357 through 361 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'D' and resid 375 through 380 removed outlier: 4.004A pdb=" N ALA D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 396 Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 12 through 20 removed outlier: 3.594A pdb=" N LYS E 18 " --> pdb=" O ALA E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 28 removed outlier: 3.560A pdb=" N PHE E 28 " --> pdb=" O SER E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 47 Processing helix chain 'E' and resid 52 through 63 Processing helix chain 'E' and resid 66 through 79 Processing helix chain 'E' and resid 86 through 118 Processing helix chain 'E' and resid 130 through 132 No H-bonds generated for 'chain 'E' and resid 130 through 132' Processing helix chain 'E' and resid 133 through 141 removed outlier: 3.534A pdb=" N ALA E 141 " --> pdb=" O ILE E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 166 Processing helix chain 'E' and resid 176 through 184 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 229 through 243 Processing helix chain 'E' and resid 246 through 251 removed outlier: 3.587A pdb=" N ASP E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 269 Processing helix chain 'E' and resid 286 through 301 Processing helix chain 'E' and resid 327 through 347 removed outlier: 3.842A pdb=" N LYS E 333 " --> pdb=" O TYR E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 361 Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 390 through 397 Processing helix chain 'F' and resid 2 through 12 Processing helix chain 'F' and resid 13 through 20 Processing helix chain 'F' and resid 21 through 23 No H-bonds generated for 'chain 'F' and resid 21 through 23' Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 31 through 48 removed outlier: 3.760A pdb=" N ASN F 35 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 62 Processing helix chain 'F' and resid 66 through 80 Processing helix chain 'F' and resid 88 through 118 removed outlier: 3.903A pdb=" N LYS F 92 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 132 No H-bonds generated for 'chain 'F' and resid 130 through 132' Processing helix chain 'F' and resid 133 through 142 removed outlier: 3.660A pdb=" N LEU F 142 " --> pdb=" O MET F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 167 Processing helix chain 'F' and resid 176 through 184 Processing helix chain 'F' and resid 202 through 216 Processing helix chain 'F' and resid 229 through 243 Processing helix chain 'F' and resid 245 through 252 Processing helix chain 'F' and resid 255 through 269 removed outlier: 3.706A pdb=" N LYS F 269 " --> pdb=" O LYS F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 302 Processing helix chain 'F' and resid 327 through 347 Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'H' and resid 4 through 18 removed outlier: 3.547A pdb=" N ASP H 8 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG H 14 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS H 18 " --> pdb=" O ARG H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 82 Processing helix chain 'H' and resid 82 through 96 removed outlier: 3.858A pdb=" N GLU H 88 " --> pdb=" O ASP H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 143 Processing helix chain 'H' and resid 146 through 152 removed outlier: 4.001A pdb=" N LYS H 151 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 167 Processing helix chain 'H' and resid 221 through 225 Processing helix chain 'H' and resid 237 through 242 removed outlier: 3.606A pdb=" N PHE H 241 " --> pdb=" O ASP H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 274 through 287 Processing helix chain 'H' and resid 303 through 312 removed outlier: 3.606A pdb=" N GLY H 312 " --> pdb=" O ILE H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 325 removed outlier: 3.738A pdb=" N ILE H 318 " --> pdb=" O THR H 314 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS H 323 " --> pdb=" O MET H 319 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN H 324 " --> pdb=" O GLU H 320 " (cutoff:3.500A) Processing helix chain 'H' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 153 removed outlier: 6.565A pdb=" N VAL B 221 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LYS B 278 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR B 223 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU B 222 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA B 353 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B 383 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS B 405 " --> pdb=" O MET B 384 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA3, first strand: chain 'A' and resid 427 through 429 removed outlier: 6.511A pdb=" N MET A 384 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU A 192 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N LEU A 385 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 194 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL A 387 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N MET A 196 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N THR A 191 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N THR A 352 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASN A 193 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ALA A 354 " --> pdb=" O ASN A 193 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU A 195 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA A 353 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU A 222 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL A 221 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LYS A 278 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TYR A 223 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 152 through 153 removed outlier: 6.614A pdb=" N VAL C 221 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LYS C 278 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TYR C 223 " --> pdb=" O LYS C 278 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASN C 220 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE C 309 " --> pdb=" O ASN C 220 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU C 222 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA C 353 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE C 383 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N MET C 384 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 172 Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 422 Processing sheet with id=AA7, first strand: chain 'C' and resid 152 through 153 removed outlier: 6.510A pdb=" N VAL D 221 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LYS D 278 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR D 223 " --> pdb=" O LYS D 278 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ILE D 309 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU D 222 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 171 through 172 Processing sheet with id=AA9, first strand: chain 'C' and resid 398 through 399 Processing sheet with id=AB1, first strand: chain 'D' and resid 152 through 153 removed outlier: 3.876A pdb=" N ALA E 353 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA E 354 " --> pdb=" O LEU E 195 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU E 192 " --> pdb=" O PHE E 383 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU E 385 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL E 194 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL E 387 " --> pdb=" O VAL E 194 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N MET E 196 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N MET E 384 " --> pdb=" O ILE E 404 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 171 through 172 Processing sheet with id=AB3, first strand: chain 'D' and resid 349 through 354 removed outlier: 6.037A pdb=" N THR D 191 " --> pdb=" O LEU D 350 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR D 352 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASN D 193 " --> pdb=" O THR D 352 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ALA D 354 " --> pdb=" O ASN D 193 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LEU D 195 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU D 192 " --> pdb=" O PHE D 383 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N LEU D 385 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL D 194 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL D 387 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N MET D 196 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N MET D 384 " --> pdb=" O ILE D 404 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 171 through 172 Processing sheet with id=AB5, first strand: chain 'F' and resid 349 through 352 removed outlier: 3.708A pdb=" N PHE F 383 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 275 through 279 removed outlier: 6.325A pdb=" N LEU F 222 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 419 through 422 Processing sheet with id=AB8, first strand: chain 'H' and resid 23 through 26 Processing sheet with id=AB9, first strand: chain 'H' and resid 124 through 126 removed outlier: 3.753A pdb=" N SER H 193 " --> pdb=" O ILE H 184 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 219 through 220 removed outlier: 3.536A pdb=" N ILE H 248 " --> pdb=" O LEU H 233 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL H 230 " --> pdb=" O VAL H 265 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 290 through 292 removed outlier: 3.508A pdb=" N ALA H 327 " --> pdb=" O VAL H 291 " (cutoff:3.500A) 1158 hydrogen bonds defined for protein. 3303 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.56 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 7549 1.35 - 1.50: 6411 1.50 - 1.65: 10008 1.65 - 1.80: 105 1.80 - 1.95: 124 Bond restraints: 24197 Sorted by residual: bond pdb=" CE1 HIS D 87 " pdb=" NE2 HIS D 87 " ideal model delta sigma weight residual 1.321 1.359 -0.038 1.00e-02 1.00e+04 1.48e+01 bond pdb=" CE1 HIS B 152 " pdb=" NE2 HIS B 152 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.24e+01 bond pdb=" N VAL E 19 " pdb=" CA VAL E 19 " ideal model delta sigma weight residual 1.452 1.492 -0.039 1.18e-02 7.18e+03 1.12e+01 bond pdb=" N TRP D 20 " pdb=" CA TRP D 20 " ideal model delta sigma weight residual 1.462 1.492 -0.030 9.50e-03 1.11e+04 9.92e+00 bond pdb=" N TRP E 20 " pdb=" CA TRP E 20 " ideal model delta sigma weight residual 1.459 1.492 -0.032 1.04e-02 9.25e+03 9.69e+00 ... (remaining 24192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 32329 2.49 - 4.98: 442 4.98 - 7.48: 28 7.48 - 9.97: 7 9.97 - 12.46: 1 Bond angle restraints: 32807 Sorted by residual: angle pdb=" PB AGS C 501 " pdb=" O3B AGS C 501 " pdb=" PG AGS C 501 " ideal model delta sigma weight residual 120.12 132.58 -12.46 3.00e+00 1.11e-01 1.73e+01 angle pdb=" N ASP A 82 " pdb=" CA ASP A 82 " pdb=" C ASP A 82 " ideal model delta sigma weight residual 112.57 108.05 4.52 1.13e+00 7.83e-01 1.60e+01 angle pdb=" N GLU H 92 " pdb=" CA GLU H 92 " pdb=" C GLU H 92 " ideal model delta sigma weight residual 111.71 107.18 4.53 1.15e+00 7.56e-01 1.55e+01 angle pdb=" CA PHE D 383 " pdb=" CB PHE D 383 " pdb=" CG PHE D 383 " ideal model delta sigma weight residual 113.80 117.73 -3.93 1.00e+00 1.00e+00 1.55e+01 angle pdb=" C GLY F 151 " pdb=" N HIS F 152 " pdb=" CA HIS F 152 " ideal model delta sigma weight residual 122.30 117.07 5.23 1.35e+00 5.49e-01 1.50e+01 ... (remaining 32802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 14414 35.65 - 71.31: 202 71.31 - 106.96: 10 106.96 - 142.62: 1 142.62 - 178.27: 4 Dihedral angle restraints: 14631 sinusoidal: 6069 harmonic: 8562 Sorted by residual: dihedral pdb=" O1B AGS E 501 " pdb=" O3B AGS E 501 " pdb=" PB AGS E 501 " pdb=" PG AGS E 501 " ideal model delta sinusoidal sigma weight residual 68.91 -112.82 -178.27 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A AGS F 501 " pdb=" O3A AGS F 501 " pdb=" PA AGS F 501 " pdb=" PB AGS F 501 " ideal model delta sinusoidal sigma weight residual -67.73 106.43 -174.16 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1B AGS B 501 " pdb=" O3B AGS B 501 " pdb=" PB AGS B 501 " pdb=" PG AGS B 501 " ideal model delta sinusoidal sigma weight residual 68.91 -88.62 157.53 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 14628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2650 0.044 - 0.088: 645 0.088 - 0.132: 288 0.132 - 0.176: 48 0.176 - 0.220: 16 Chirality restraints: 3647 Sorted by residual: chirality pdb=" CA ILE H 93 " pdb=" N ILE H 93 " pdb=" C ILE H 93 " pdb=" CB ILE H 93 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA VAL A 150 " pdb=" N VAL A 150 " pdb=" C VAL A 150 " pdb=" CB VAL A 150 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ARG A 124 " pdb=" N ARG A 124 " pdb=" C ARG A 124 " pdb=" CB ARG A 124 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 3644 not shown) Planarity restraints: 4071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 266 " 0.018 2.00e-02 2.50e+03 2.32e-02 1.35e+01 pdb=" CG TRP H 266 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP H 266 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP H 266 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 266 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP H 266 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP H 266 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 266 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 266 " 0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP H 266 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 373 " -0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C GLU A 373 " 0.057 2.00e-02 2.50e+03 pdb=" O GLU A 373 " -0.021 2.00e-02 2.50e+03 pdb=" N SER A 374 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 145 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C SER B 145 " 0.039 2.00e-02 2.50e+03 pdb=" O SER B 145 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE B 146 " -0.013 2.00e-02 2.50e+03 ... (remaining 4068 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 113 2.47 - 3.07: 16357 3.07 - 3.68: 36394 3.68 - 4.29: 55354 4.29 - 4.90: 90583 Nonbonded interactions: 198801 Sorted by model distance: nonbonded pdb=" O1B AGS C 501 " pdb="MG MG C 502 " model vdw 1.856 2.170 nonbonded pdb=" O3B AGS B 501 " pdb="MG MG B 502 " model vdw 1.972 2.170 nonbonded pdb=" OE2 GLU B 227 " pdb="MG MG B 502 " model vdw 1.979 2.170 nonbonded pdb=" O2G AGS E 501 " pdb="MG MG E 502 " model vdw 1.985 2.170 nonbonded pdb=" O2B AGS F 501 " pdb="MG MG F 502 " model vdw 1.993 2.170 ... (remaining 198796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 432) selection = (chain 'C' and resid 1 through 432) selection = (chain 'D' and resid 1 through 432) selection = (chain 'E' and resid 1 through 432) selection = (chain 'F' and resid 1 through 432) } 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: 2.160 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.940 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 0.051 24197 Z= 0.307 Angle : 0.682 12.461 32807 Z= 0.446 Chirality : 0.049 0.220 3647 Planarity : 0.004 0.075 4071 Dihedral : 12.486 178.275 9101 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.78 % Allowed : 7.25 % Favored : 90.96 % 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 aren not related in a simple way. whole: 0.23 (0.16), residues: 2898 helix: 1.29 (0.14), residues: 1435 sheet: -0.35 (0.27), residues: 407 loop : -1.20 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 87 TYR 0.014 0.001 TYR E 329 PHE 0.022 0.002 PHE D 383 TRP 0.059 0.001 TRP H 266 HIS 0.008 0.001 HIS B 152 Details of bonding type rmsd covalent geometry : bond 0.00449 (24197) covalent geometry : angle 0.68203 (32807) hydrogen bonds : bond 0.15957 ( 1158) hydrogen bonds : angle 6.57570 ( 3303) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 722 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7054 (m) cc_final: 0.6730 (t) REVERT: A 327 ASN cc_start: 0.3766 (OUTLIER) cc_final: 0.3371 (p0) REVERT: A 347 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7664 (mm-30) REVERT: A 368 MET cc_start: 0.6148 (OUTLIER) cc_final: 0.5815 (ttm) REVERT: A 369 SER cc_start: 0.5907 (m) cc_final: 0.5493 (p) REVERT: B 48 HIS cc_start: 0.7610 (m90) cc_final: 0.7105 (m90) REVERT: B 96 LYS cc_start: 0.8324 (mtpp) cc_final: 0.8100 (mtpp) REVERT: B 267 ARG cc_start: 0.7854 (ttp-170) cc_final: 0.7588 (ttp-170) REVERT: B 422 GLN cc_start: 0.6749 (mt0) cc_final: 0.6413 (mm-40) REVERT: C 128 MET cc_start: 0.5747 (tpp) cc_final: 0.5430 (mmt) REVERT: C 323 VAL cc_start: 0.7577 (t) cc_final: 0.7044 (t) REVERT: D 26 GLU cc_start: 0.7746 (mp0) cc_final: 0.7446 (mm-30) REVERT: D 265 LYS cc_start: 0.7855 (ttmm) cc_final: 0.7464 (tmmt) REVERT: E 109 LYS cc_start: 0.7506 (tptt) cc_final: 0.7222 (ttmt) REVERT: E 338 GLU cc_start: 0.6474 (mt-10) cc_final: 0.6217 (mp0) REVERT: E 380 THR cc_start: 0.8287 (OUTLIER) cc_final: 0.7935 (p) REVERT: F 128 MET cc_start: 0.6055 (ttt) cc_final: 0.5835 (ttm) REVERT: F 156 ASP cc_start: 0.7667 (t0) cc_final: 0.7429 (t0) REVERT: F 167 ASN cc_start: 0.6020 (OUTLIER) cc_final: 0.4854 (m-40) REVERT: F 213 ASP cc_start: 0.7586 (m-30) cc_final: 0.7311 (m-30) REVERT: F 276 ILE cc_start: 0.8836 (mt) cc_final: 0.8629 (tt) REVERT: F 345 GLU cc_start: 0.7727 (tt0) cc_final: 0.7486 (tt0) REVERT: F 355 GLN cc_start: 0.6770 (tt0) cc_final: 0.6484 (pm20) REVERT: F 399 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.6922 (tp40) REVERT: F 423 LYS cc_start: 0.8029 (mttm) cc_final: 0.7779 (mttp) REVERT: H 161 LYS cc_start: 0.4172 (tmmt) cc_final: 0.3864 (mttt) REVERT: H 283 LYS cc_start: 0.7693 (tttt) cc_final: 0.7450 (mtmt) REVERT: H 294 TRP cc_start: 0.7286 (m100) cc_final: 0.7085 (m100) REVERT: H 305 ASN cc_start: 0.6222 (t0) cc_final: 0.5936 (t0) REVERT: H 307 MET cc_start: 0.6672 (mtt) cc_final: 0.6405 (mtt) outliers start: 45 outliers final: 4 residues processed: 750 average time/residue: 0.1724 time to fit residues: 190.6337 Evaluate side-chains 381 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 372 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN A 140 GLN A 167 ASN A 288 ASN A 327 ASN B 253 HIS ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS C 114 GLN ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN C 288 ASN C 295 ASN D 48 HIS D 116 ASN D 200 ASN E 114 GLN F 8 HIS F 62 ASN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 ASN H 325 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.144296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.116722 restraints weight = 38578.081| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.10 r_work: 0.3320 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 24197 Z= 0.134 Angle : 0.555 8.015 32807 Z= 0.301 Chirality : 0.042 0.245 3647 Planarity : 0.004 0.048 4071 Dihedral : 10.815 174.900 3415 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.90 % Allowed : 11.10 % Favored : 87.00 % 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 aren not related in a simple way. whole: 0.42 (0.16), residues: 2898 helix: 1.44 (0.14), residues: 1458 sheet: -0.28 (0.27), residues: 406 loop : -1.14 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 124 TYR 0.017 0.001 TYR H 213 PHE 0.016 0.002 PHE D 65 TRP 0.018 0.001 TRP H 266 HIS 0.011 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00294 (24197) covalent geometry : angle 0.55546 (32807) hydrogen bonds : bond 0.04068 ( 1158) hydrogen bonds : angle 5.13285 ( 3303) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 396 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.6632 (tp30) cc_final: 0.6378 (tt0) REVERT: A 263 MET cc_start: 0.6996 (mmm) cc_final: 0.6706 (mmm) REVERT: A 330 THR cc_start: 0.7593 (m) cc_final: 0.7312 (t) REVERT: A 369 SER cc_start: 0.6147 (m) cc_final: 0.5757 (p) REVERT: B 48 HIS cc_start: 0.7640 (m90) cc_final: 0.7370 (m90) REVERT: B 124 ARG cc_start: 0.7150 (tpp80) cc_final: 0.6939 (tpp80) REVERT: B 422 GLN cc_start: 0.6891 (mt0) cc_final: 0.6476 (mm-40) REVERT: C 13 GLN cc_start: 0.7759 (tp40) cc_final: 0.7188 (tp-100) REVERT: C 69 GLU cc_start: 0.7261 (pt0) cc_final: 0.6419 (mm-30) REVERT: C 128 MET cc_start: 0.5972 (tpp) cc_final: 0.5511 (mmt) REVERT: C 158 TYR cc_start: 0.6949 (p90) cc_final: 0.6679 (p90) REVERT: D 26 GLU cc_start: 0.8213 (mp0) cc_final: 0.7827 (mm-30) REVERT: D 92 LYS cc_start: 0.8105 (mtmt) cc_final: 0.7894 (mmmm) REVERT: D 247 ASP cc_start: 0.7753 (m-30) cc_final: 0.7484 (t70) REVERT: E 306 THR cc_start: 0.8222 (m) cc_final: 0.7849 (t) REVERT: E 338 GLU cc_start: 0.6744 (mt-10) cc_final: 0.6363 (mp0) REVERT: F 167 ASN cc_start: 0.6027 (OUTLIER) cc_final: 0.4971 (m-40) REVERT: F 213 ASP cc_start: 0.7555 (m-30) cc_final: 0.7262 (m-30) REVERT: F 227 GLU cc_start: 0.7095 (pt0) cc_final: 0.6653 (tt0) REVERT: F 355 GLN cc_start: 0.7463 (tt0) cc_final: 0.7048 (pm20) REVERT: F 399 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7093 (tp40) REVERT: H 141 LYS cc_start: 0.5242 (pttt) cc_final: 0.4977 (ttmt) REVERT: H 161 LYS cc_start: 0.3952 (tmmt) cc_final: 0.3554 (mmtt) REVERT: H 292 MET cc_start: 0.7571 (tpp) cc_final: 0.6274 (tpt) outliers start: 48 outliers final: 21 residues processed: 431 average time/residue: 0.1751 time to fit residues: 115.0331 Evaluate side-chains 336 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 313 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 85 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 154 optimal weight: 7.9990 chunk 244 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 140 GLN A 422 GLN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN D 13 GLN D 48 HIS D 200 ASN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 252 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.141582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112353 restraints weight = 38462.425| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.19 r_work: 0.3242 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24197 Z= 0.148 Angle : 0.553 9.712 32807 Z= 0.296 Chirality : 0.043 0.263 3647 Planarity : 0.004 0.050 4071 Dihedral : 10.748 176.487 3407 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.38 % Allowed : 11.97 % Favored : 85.65 % 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 aren not related in a simple way. whole: 0.51 (0.16), residues: 2898 helix: 1.56 (0.14), residues: 1449 sheet: -0.16 (0.27), residues: 403 loop : -1.17 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 274 TYR 0.016 0.001 TYR H 86 PHE 0.016 0.002 PHE C 37 TRP 0.015 0.001 TRP E 20 HIS 0.007 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00334 (24197) covalent geometry : angle 0.55331 (32807) hydrogen bonds : bond 0.03728 ( 1158) hydrogen bonds : angle 4.94303 ( 3303) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 344 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.7069 (mmm) cc_final: 0.6693 (mmm) REVERT: A 330 THR cc_start: 0.7585 (m) cc_final: 0.7354 (t) REVERT: A 380 THR cc_start: 0.7869 (p) cc_final: 0.7262 (t) REVERT: B 48 HIS cc_start: 0.7620 (m90) cc_final: 0.7313 (m90) REVERT: B 155 MET cc_start: 0.8691 (tpp) cc_final: 0.8381 (tpt) REVERT: B 422 GLN cc_start: 0.6835 (mt0) cc_final: 0.6486 (mm-40) REVERT: C 69 GLU cc_start: 0.7283 (pt0) cc_final: 0.6389 (mm-30) REVERT: C 128 MET cc_start: 0.5864 (tpp) cc_final: 0.5379 (mmt) REVERT: C 138 MET cc_start: 0.7315 (tpt) cc_final: 0.7083 (tpt) REVERT: D 26 GLU cc_start: 0.8024 (mp0) cc_final: 0.7775 (mm-30) REVERT: D 247 ASP cc_start: 0.7601 (m-30) cc_final: 0.7344 (t70) REVERT: E 24 ASP cc_start: 0.6618 (m-30) cc_final: 0.6355 (m-30) REVERT: E 118 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7621 (tm-30) REVERT: E 306 THR cc_start: 0.8300 (m) cc_final: 0.7876 (t) REVERT: E 338 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6180 (mp0) REVERT: F 167 ASN cc_start: 0.6115 (OUTLIER) cc_final: 0.4992 (m110) REVERT: F 355 GLN cc_start: 0.7237 (tt0) cc_final: 0.6994 (pm20) REVERT: F 399 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7108 (tp40) REVERT: H 34 ARG cc_start: 0.3569 (ttt180) cc_final: 0.2965 (ttm170) REVERT: H 88 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6108 (mm-30) REVERT: H 141 LYS cc_start: 0.5381 (pttt) cc_final: 0.5114 (ttmt) REVERT: H 218 LYS cc_start: 0.5505 (mtmt) cc_final: 0.5165 (ttpt) REVERT: H 263 ARG cc_start: 0.6353 (ptt90) cc_final: 0.6138 (ptt90) REVERT: H 292 MET cc_start: 0.7783 (tpp) cc_final: 0.6284 (tpt) outliers start: 60 outliers final: 40 residues processed: 388 average time/residue: 0.1921 time to fit residues: 114.0804 Evaluate side-chains 346 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 302 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 282 THR Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 194 optimal weight: 9.9990 chunk 236 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 268 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 289 optimal weight: 3.9990 chunk 288 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 285 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 140 GLN A 403 GLN B 355 GLN C 35 ASN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN D 48 HIS D 114 GLN F 167 ASN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.139050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.110470 restraints weight = 38519.555| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.15 r_work: 0.3204 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24197 Z= 0.178 Angle : 0.581 10.382 32807 Z= 0.312 Chirality : 0.043 0.273 3647 Planarity : 0.004 0.037 4071 Dihedral : 10.883 175.305 3405 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.05 % Allowed : 13.12 % Favored : 83.83 % 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 aren not related in a simple way. whole: 0.42 (0.16), residues: 2898 helix: 1.45 (0.14), residues: 1450 sheet: -0.18 (0.27), residues: 393 loop : -1.17 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 273 TYR 0.017 0.002 TYR D 329 PHE 0.017 0.002 PHE H 81 TRP 0.016 0.002 TRP D 162 HIS 0.006 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00411 (24197) covalent geometry : angle 0.58105 (32807) hydrogen bonds : bond 0.03775 ( 1158) hydrogen bonds : angle 4.90253 ( 3303) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 321 time to evaluate : 0.976 Fit side-chains REVERT: A 263 MET cc_start: 0.7243 (mmm) cc_final: 0.6860 (mmm) REVERT: B 48 HIS cc_start: 0.7828 (m90) cc_final: 0.7600 (m90) REVERT: B 155 MET cc_start: 0.8768 (tpp) cc_final: 0.8435 (tpt) REVERT: B 248 ASP cc_start: 0.8059 (m-30) cc_final: 0.7814 (m-30) REVERT: B 422 GLN cc_start: 0.7160 (mt0) cc_final: 0.6845 (mm-40) REVERT: C 69 GLU cc_start: 0.7320 (pt0) cc_final: 0.6343 (mm-30) REVERT: C 128 MET cc_start: 0.5829 (tpp) cc_final: 0.5342 (mmt) REVERT: D 26 GLU cc_start: 0.8358 (mp0) cc_final: 0.8063 (mm-30) REVERT: D 136 ASP cc_start: 0.7512 (t0) cc_final: 0.7281 (m-30) REVERT: D 247 ASP cc_start: 0.7748 (m-30) cc_final: 0.7431 (t70) REVERT: E 24 ASP cc_start: 0.6979 (m-30) cc_final: 0.6777 (m-30) REVERT: E 100 GLN cc_start: 0.8344 (tm-30) cc_final: 0.8064 (tm-30) REVERT: E 118 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7779 (tm-30) REVERT: E 296 GLU cc_start: 0.6375 (mt-10) cc_final: 0.6100 (mt-10) REVERT: E 338 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6278 (mp0) REVERT: E 377 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8057 (mp) REVERT: F 131 VAL cc_start: 0.8297 (OUTLIER) cc_final: 0.8046 (p) REVERT: F 367 ASN cc_start: 0.6641 (p0) cc_final: 0.6093 (m-40) REVERT: H 34 ARG cc_start: 0.3659 (ttt180) cc_final: 0.3049 (ttm170) REVERT: H 88 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6191 (mm-30) REVERT: H 141 LYS cc_start: 0.5160 (pttp) cc_final: 0.4824 (ttmt) REVERT: H 263 ARG cc_start: 0.6449 (ptt90) cc_final: 0.6173 (ptt90) REVERT: H 292 MET cc_start: 0.8172 (tpp) cc_final: 0.7308 (tpt) outliers start: 77 outliers final: 55 residues processed: 380 average time/residue: 0.1753 time to fit residues: 103.8324 Evaluate side-chains 359 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 300 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 359 GLN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 318 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 3 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 283 optimal weight: 3.9990 chunk 253 optimal weight: 10.0000 chunk 282 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 266 optimal weight: 0.9990 chunk 281 optimal weight: 8.9990 chunk 172 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 226 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS C 35 ASN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN D 48 HIS D 114 GLN D 200 ASN E 114 GLN F 13 GLN F 125 ASN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.139662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.111695 restraints weight = 38238.657| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.11 r_work: 0.3226 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24197 Z= 0.132 Angle : 0.534 10.444 32807 Z= 0.285 Chirality : 0.042 0.249 3647 Planarity : 0.004 0.035 4071 Dihedral : 10.781 175.433 3405 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.50 % Allowed : 14.31 % Favored : 83.19 % 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 aren not related in a simple way. whole: 0.56 (0.16), residues: 2898 helix: 1.57 (0.14), residues: 1450 sheet: -0.06 (0.27), residues: 377 loop : -1.14 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 291 TYR 0.022 0.001 TYR D 312 PHE 0.024 0.002 PHE C 37 TRP 0.014 0.001 TRP D 162 HIS 0.006 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00299 (24197) covalent geometry : angle 0.53450 (32807) hydrogen bonds : bond 0.03424 ( 1158) hydrogen bonds : angle 4.76550 ( 3303) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 319 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 263 MET cc_start: 0.7350 (mmm) cc_final: 0.6952 (mmm) REVERT: B 48 HIS cc_start: 0.7836 (m90) cc_final: 0.7612 (m90) REVERT: B 248 ASP cc_start: 0.8045 (m-30) cc_final: 0.7804 (m-30) REVERT: C 23 MET cc_start: 0.8275 (tpp) cc_final: 0.8030 (tpp) REVERT: C 69 GLU cc_start: 0.7270 (pt0) cc_final: 0.6360 (mm-30) REVERT: C 128 MET cc_start: 0.5852 (tpp) cc_final: 0.5346 (mmt) REVERT: D 247 ASP cc_start: 0.7760 (m-30) cc_final: 0.7490 (t70) REVERT: E 23 MET cc_start: 0.8499 (mmt) cc_final: 0.8283 (mmt) REVERT: E 77 ILE cc_start: 0.7997 (pt) cc_final: 0.7326 (mt) REVERT: E 118 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7768 (tm-30) REVERT: E 124 ARG cc_start: 0.5186 (ptp-170) cc_final: 0.4765 (mtm110) REVERT: E 269 LYS cc_start: 0.8335 (mttm) cc_final: 0.7939 (mtpt) REVERT: E 296 GLU cc_start: 0.6251 (mt-10) cc_final: 0.6035 (mt-10) REVERT: E 306 THR cc_start: 0.8274 (m) cc_final: 0.7844 (t) REVERT: E 338 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6235 (mp0) REVERT: E 377 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7992 (mp) REVERT: F 367 ASN cc_start: 0.6648 (p0) cc_final: 0.6212 (m-40) REVERT: H 34 ARG cc_start: 0.3771 (ttt180) cc_final: 0.3171 (ttm170) REVERT: H 88 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6187 (mm-30) REVERT: H 141 LYS cc_start: 0.5011 (pttp) cc_final: 0.4662 (ttmt) REVERT: H 292 MET cc_start: 0.8198 (tpp) cc_final: 0.7455 (tpt) outliers start: 63 outliers final: 42 residues processed: 369 average time/residue: 0.1755 time to fit residues: 100.6150 Evaluate side-chains 337 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 292 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 64 optimal weight: 5.9990 chunk 192 optimal weight: 0.8980 chunk 252 optimal weight: 0.2980 chunk 55 optimal weight: 5.9990 chunk 181 optimal weight: 0.8980 chunk 229 optimal weight: 0.0010 chunk 36 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 235 optimal weight: 8.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 HIS D 200 ASN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 325 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.140365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.111878 restraints weight = 38572.368| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.14 r_work: 0.3239 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24197 Z= 0.104 Angle : 0.508 10.870 32807 Z= 0.272 Chirality : 0.041 0.237 3647 Planarity : 0.003 0.038 4071 Dihedral : 10.629 174.742 3405 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.02 % Allowed : 14.67 % Favored : 83.31 % 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 aren not related in a simple way. whole: 0.66 (0.16), residues: 2898 helix: 1.71 (0.14), residues: 1448 sheet: -0.01 (0.28), residues: 379 loop : -1.17 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 124 TYR 0.024 0.001 TYR D 329 PHE 0.015 0.001 PHE C 37 TRP 0.014 0.001 TRP F 89 HIS 0.005 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00221 (24197) covalent geometry : angle 0.50772 (32807) hydrogen bonds : bond 0.03142 ( 1158) hydrogen bonds : angle 4.63557 ( 3303) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 322 time to evaluate : 0.907 Fit side-chains REVERT: A 263 MET cc_start: 0.7338 (mmm) cc_final: 0.6942 (mmm) REVERT: B 139 ARG cc_start: 0.7701 (ttm-80) cc_final: 0.7434 (ptp90) REVERT: B 248 ASP cc_start: 0.7942 (m-30) cc_final: 0.7734 (m-30) REVERT: C 69 GLU cc_start: 0.7258 (pt0) cc_final: 0.6367 (mm-30) REVERT: C 128 MET cc_start: 0.5722 (tpp) cc_final: 0.5235 (mmt) REVERT: D 247 ASP cc_start: 0.7758 (m-30) cc_final: 0.7482 (t70) REVERT: E 77 ILE cc_start: 0.8068 (pt) cc_final: 0.7477 (mt) REVERT: E 118 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: E 269 LYS cc_start: 0.8347 (mttm) cc_final: 0.7909 (mmtm) REVERT: E 306 THR cc_start: 0.8280 (m) cc_final: 0.7863 (t) REVERT: E 338 GLU cc_start: 0.6896 (mt-10) cc_final: 0.6252 (mp0) REVERT: F 367 ASN cc_start: 0.6728 (p0) cc_final: 0.6255 (m-40) REVERT: F 399 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7303 (tp40) REVERT: H 34 ARG cc_start: 0.3721 (ttt180) cc_final: 0.3154 (ttm170) REVERT: H 88 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6213 (mm-30) REVERT: H 141 LYS cc_start: 0.5165 (pttp) cc_final: 0.4816 (ttmt) REVERT: H 292 MET cc_start: 0.8187 (tpp) cc_final: 0.7454 (tpt) REVERT: H 305 ASN cc_start: 0.5655 (t0) cc_final: 0.5032 (p0) REVERT: H 309 ARG cc_start: 0.5698 (OUTLIER) cc_final: 0.5335 (ptt180) outliers start: 51 outliers final: 39 residues processed: 362 average time/residue: 0.1839 time to fit residues: 102.8868 Evaluate side-chains 338 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 295 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 359 GLN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 222 VAL Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 309 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 233 optimal weight: 20.0000 chunk 72 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 246 optimal weight: 10.0000 chunk 286 optimal weight: 0.7980 chunk 256 optimal weight: 7.9990 chunk 269 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS B 87 HIS ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN D 200 ASN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.139290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.111217 restraints weight = 38263.350| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.11 r_work: 0.3224 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24197 Z= 0.146 Angle : 0.540 9.674 32807 Z= 0.289 Chirality : 0.042 0.227 3647 Planarity : 0.004 0.039 4071 Dihedral : 10.759 175.550 3405 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.54 % Allowed : 14.27 % Favored : 83.19 % 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 aren not related in a simple way. whole: 0.59 (0.16), residues: 2898 helix: 1.62 (0.14), residues: 1448 sheet: -0.04 (0.28), residues: 377 loop : -1.17 (0.18), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 124 TYR 0.023 0.001 TYR D 329 PHE 0.024 0.002 PHE C 104 TRP 0.013 0.001 TRP D 162 HIS 0.005 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00337 (24197) covalent geometry : angle 0.54047 (32807) hydrogen bonds : bond 0.03361 ( 1158) hydrogen bonds : angle 4.70456 ( 3303) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 304 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: A 263 MET cc_start: 0.7320 (mmm) cc_final: 0.6950 (mmm) REVERT: B 248 ASP cc_start: 0.8112 (m-30) cc_final: 0.7838 (m-30) REVERT: C 69 GLU cc_start: 0.7278 (pt0) cc_final: 0.6387 (mm-30) REVERT: C 103 MET cc_start: 0.8315 (mmm) cc_final: 0.8100 (mmm) REVERT: C 128 MET cc_start: 0.5812 (tpp) cc_final: 0.5253 (mmt) REVERT: D 108 SER cc_start: 0.8628 (m) cc_final: 0.8410 (t) REVERT: D 247 ASP cc_start: 0.7637 (m-30) cc_final: 0.7402 (t70) REVERT: E 77 ILE cc_start: 0.8047 (pt) cc_final: 0.7444 (mt) REVERT: E 128 MET cc_start: 0.7169 (mmm) cc_final: 0.6849 (mtp) REVERT: E 269 LYS cc_start: 0.8348 (mttm) cc_final: 0.7892 (mmtm) REVERT: E 338 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6227 (mp0) REVERT: F 274 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7828 (mtp-110) REVERT: F 367 ASN cc_start: 0.6712 (p0) cc_final: 0.6277 (m-40) REVERT: H 88 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6176 (mm-30) REVERT: H 141 LYS cc_start: 0.5148 (pttp) cc_final: 0.4741 (ttmt) REVERT: H 197 ARG cc_start: 0.3627 (tpt170) cc_final: 0.3119 (tpt90) REVERT: H 292 MET cc_start: 0.8289 (tpp) cc_final: 0.7513 (tpt) REVERT: H 305 ASN cc_start: 0.5313 (t0) cc_final: 0.5038 (p0) REVERT: H 309 ARG cc_start: 0.5706 (OUTLIER) cc_final: 0.5429 (ptt180) outliers start: 64 outliers final: 47 residues processed: 353 average time/residue: 0.1794 time to fit residues: 98.2476 Evaluate side-chains 336 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 287 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 359 GLN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 309 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 203 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 252 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 166 optimal weight: 30.0000 chunk 47 optimal weight: 6.9990 chunk 247 optimal weight: 7.9990 chunk 143 optimal weight: 0.0030 chunk 237 optimal weight: 10.0000 overall best weight: 4.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 HIS ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 HIS H 274 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.136492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.108552 restraints weight = 38498.552| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.13 r_work: 0.3181 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 24197 Z= 0.221 Angle : 0.631 11.544 32807 Z= 0.336 Chirality : 0.045 0.188 3647 Planarity : 0.004 0.042 4071 Dihedral : 11.092 177.802 3405 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.58 % Allowed : 14.55 % Favored : 82.88 % 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 aren not related in a simple way. whole: 0.25 (0.16), residues: 2898 helix: 1.32 (0.14), residues: 1451 sheet: -0.27 (0.27), residues: 388 loop : -1.27 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 291 TYR 0.036 0.002 TYR D 312 PHE 0.027 0.002 PHE C 104 TRP 0.018 0.002 TRP D 162 HIS 0.006 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00521 (24197) covalent geometry : angle 0.63112 (32807) hydrogen bonds : bond 0.03869 ( 1158) hydrogen bonds : angle 4.93291 ( 3303) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 299 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7609 (mt-10) REVERT: A 259 TYR cc_start: 0.7545 (t80) cc_final: 0.7062 (t80) REVERT: A 263 MET cc_start: 0.7408 (mmm) cc_final: 0.7179 (mmm) REVERT: C 69 GLU cc_start: 0.7269 (pt0) cc_final: 0.6380 (mm-30) REVERT: C 128 MET cc_start: 0.5840 (tpp) cc_final: 0.5281 (mmt) REVERT: D 108 SER cc_start: 0.8644 (m) cc_final: 0.8443 (t) REVERT: D 247 ASP cc_start: 0.7619 (m-30) cc_final: 0.7400 (t70) REVERT: E 77 ILE cc_start: 0.8111 (pt) cc_final: 0.7492 (mt) REVERT: E 128 MET cc_start: 0.7203 (mmm) cc_final: 0.6943 (mtp) REVERT: E 269 LYS cc_start: 0.8348 (mttm) cc_final: 0.7860 (mmtm) REVERT: E 338 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6792 (mt-10) REVERT: F 367 ASN cc_start: 0.6687 (p0) cc_final: 0.6336 (m-40) REVERT: H 49 LYS cc_start: 0.1281 (mttt) cc_final: 0.0805 (ptpt) REVERT: H 88 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6231 (mm-30) REVERT: H 141 LYS cc_start: 0.5225 (pttp) cc_final: 0.4821 (ttmt) REVERT: H 292 MET cc_start: 0.8423 (tpp) cc_final: 0.8032 (tpp) REVERT: H 309 ARG cc_start: 0.5760 (OUTLIER) cc_final: 0.5466 (ptt180) outliers start: 65 outliers final: 55 residues processed: 354 average time/residue: 0.1482 time to fit residues: 81.8894 Evaluate side-chains 345 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 287 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 359 GLN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 309 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 116 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 276 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 179 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN F 253 HIS ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.138519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.110609 restraints weight = 38467.409| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.12 r_work: 0.3219 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24197 Z= 0.131 Angle : 0.552 10.056 32807 Z= 0.295 Chirality : 0.042 0.174 3647 Planarity : 0.004 0.041 4071 Dihedral : 10.916 177.508 3405 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.10 % Allowed : 14.98 % Favored : 82.92 % 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 aren not related in a simple way. whole: 0.43 (0.16), residues: 2898 helix: 1.52 (0.14), residues: 1449 sheet: -0.16 (0.28), residues: 388 loop : -1.28 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 274 TYR 0.032 0.001 TYR D 312 PHE 0.027 0.002 PHE C 104 TRP 0.017 0.001 TRP D 162 HIS 0.005 0.001 HIS F 253 Details of bonding type rmsd covalent geometry : bond 0.00296 (24197) covalent geometry : angle 0.55230 (32807) hydrogen bonds : bond 0.03335 ( 1158) hydrogen bonds : angle 4.74335 ( 3303) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 301 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 259 TYR cc_start: 0.7513 (t80) cc_final: 0.7300 (t80) REVERT: A 263 MET cc_start: 0.7400 (mmm) cc_final: 0.6987 (mmm) REVERT: B 158 TYR cc_start: 0.8148 (p90) cc_final: 0.7713 (p90) REVERT: B 312 TYR cc_start: 0.7188 (t80) cc_final: 0.6911 (t80) REVERT: C 35 ASN cc_start: 0.6364 (m-40) cc_final: 0.5936 (m110) REVERT: C 38 LYS cc_start: 0.7846 (mtmt) cc_final: 0.7324 (ptpt) REVERT: C 69 GLU cc_start: 0.7246 (pt0) cc_final: 0.6370 (mm-30) REVERT: C 115 THR cc_start: 0.7506 (m) cc_final: 0.7268 (p) REVERT: C 128 MET cc_start: 0.5780 (tpp) cc_final: 0.5369 (mmt) REVERT: D 247 ASP cc_start: 0.7636 (m-30) cc_final: 0.7410 (t70) REVERT: D 298 LYS cc_start: 0.7277 (ttpt) cc_final: 0.6543 (ptmt) REVERT: E 112 GLU cc_start: 0.8184 (tt0) cc_final: 0.7844 (tt0) REVERT: E 128 MET cc_start: 0.7104 (mmm) cc_final: 0.6815 (mtp) REVERT: E 269 LYS cc_start: 0.8323 (mttm) cc_final: 0.7900 (mmtm) REVERT: E 338 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6696 (mt-10) REVERT: F 114 GLN cc_start: 0.8542 (mt0) cc_final: 0.8287 (mt0) REVERT: F 367 ASN cc_start: 0.6731 (p0) cc_final: 0.6355 (m-40) REVERT: H 34 ARG cc_start: 0.3990 (ttt180) cc_final: 0.3334 (ttm170) REVERT: H 49 LYS cc_start: 0.1383 (mttt) cc_final: 0.0795 (ptpt) REVERT: H 88 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6217 (mm-30) REVERT: H 141 LYS cc_start: 0.5229 (pttp) cc_final: 0.4810 (ttmt) REVERT: H 292 MET cc_start: 0.8423 (tpp) cc_final: 0.7999 (tpp) REVERT: H 309 ARG cc_start: 0.5782 (OUTLIER) cc_final: 0.5518 (ptt180) outliers start: 53 outliers final: 43 residues processed: 343 average time/residue: 0.1692 time to fit residues: 89.4598 Evaluate side-chains 329 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 284 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 359 GLN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 309 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 242 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 179 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 208 optimal weight: 7.9990 chunk 241 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 184 optimal weight: 0.0030 overall best weight: 2.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN D 412 ASN F 253 HIS ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.137829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.109354 restraints weight = 38538.643| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.21 r_work: 0.3196 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24197 Z= 0.152 Angle : 0.572 10.650 32807 Z= 0.304 Chirality : 0.042 0.176 3647 Planarity : 0.004 0.041 4071 Dihedral : 10.939 177.587 3405 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.94 % Allowed : 15.22 % Favored : 82.84 % 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 aren not related in a simple way. whole: 0.43 (0.16), residues: 2898 helix: 1.52 (0.14), residues: 1446 sheet: -0.15 (0.28), residues: 384 loop : -1.28 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 291 TYR 0.033 0.002 TYR D 312 PHE 0.027 0.002 PHE C 104 TRP 0.015 0.001 TRP D 162 HIS 0.006 0.001 HIS F 253 Details of bonding type rmsd covalent geometry : bond 0.00350 (24197) covalent geometry : angle 0.57234 (32807) hydrogen bonds : bond 0.03452 ( 1158) hydrogen bonds : angle 4.76595 ( 3303) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 290 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 259 TYR cc_start: 0.7545 (t80) cc_final: 0.7305 (t80) REVERT: A 263 MET cc_start: 0.7431 (mmm) cc_final: 0.7025 (mmm) REVERT: B 139 ARG cc_start: 0.7816 (ttm-80) cc_final: 0.7498 (ptp90) REVERT: B 158 TYR cc_start: 0.8175 (p90) cc_final: 0.7711 (p90) REVERT: B 312 TYR cc_start: 0.7322 (t80) cc_final: 0.7086 (t80) REVERT: C 69 GLU cc_start: 0.7279 (pt0) cc_final: 0.6427 (mm-30) REVERT: C 115 THR cc_start: 0.7445 (m) cc_final: 0.7210 (p) REVERT: C 128 MET cc_start: 0.5821 (tpp) cc_final: 0.5394 (mmt) REVERT: D 247 ASP cc_start: 0.7609 (m-30) cc_final: 0.7334 (t70) REVERT: D 293 LEU cc_start: 0.7695 (tp) cc_final: 0.7413 (tp) REVERT: D 298 LYS cc_start: 0.7267 (ttpt) cc_final: 0.6577 (ptmt) REVERT: E 112 GLU cc_start: 0.8249 (tt0) cc_final: 0.7885 (tt0) REVERT: E 128 MET cc_start: 0.7172 (mmm) cc_final: 0.6948 (mtp) REVERT: E 269 LYS cc_start: 0.8362 (mttm) cc_final: 0.7871 (mmtm) REVERT: F 114 GLN cc_start: 0.8556 (mt0) cc_final: 0.8266 (mt0) REVERT: F 367 ASN cc_start: 0.6603 (p0) cc_final: 0.6376 (m-40) REVERT: H 49 LYS cc_start: 0.1652 (mttt) cc_final: 0.1041 (ptpt) REVERT: H 88 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6216 (mm-30) REVERT: H 292 MET cc_start: 0.8413 (tpp) cc_final: 0.7996 (tpp) REVERT: H 309 ARG cc_start: 0.5781 (OUTLIER) cc_final: 0.5519 (ptt180) outliers start: 49 outliers final: 42 residues processed: 331 average time/residue: 0.1619 time to fit residues: 84.0899 Evaluate side-chains 322 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 278 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 359 GLN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 309 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 52 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 96 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 273 optimal weight: 5.9990 chunk 226 optimal weight: 7.9990 chunk 251 optimal weight: 0.2980 chunk 88 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN E 253 HIS F 253 HIS ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.137886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.109875 restraints weight = 38411.984| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.15 r_work: 0.3208 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.225 24197 Z= 0.197 Angle : 0.710 59.191 32807 Z= 0.405 Chirality : 0.047 1.266 3647 Planarity : 0.004 0.042 4071 Dihedral : 10.937 177.603 3405 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.98 % Allowed : 15.34 % Favored : 82.68 % Cbeta Deviations : 0.04 % 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 aren not related in a simple way. whole: 0.43 (0.16), residues: 2898 helix: 1.53 (0.14), residues: 1447 sheet: -0.15 (0.28), residues: 384 loop : -1.29 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 291 TYR 0.028 0.001 TYR D 312 PHE 0.025 0.002 PHE C 104 TRP 0.015 0.001 TRP D 162 HIS 0.005 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00398 (24197) covalent geometry : angle 0.70956 (32807) hydrogen bonds : bond 0.03421 ( 1158) hydrogen bonds : angle 4.76430 ( 3303) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6546.01 seconds wall clock time: 113 minutes 1.99 seconds (6781.99 seconds total)