Starting phenix.real_space_refine on Sun Sep 13 13:11:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dvi_27739/09_2026/8dvi_27739.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dvi_27739/09_2026/8dvi_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_27739/09_2026/8dvi_27739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dvi_27739/09_2026/8dvi_27739.map" model { file = "/net/cci-nas-00/data/ceres_data/8dvi_27739/09_2026/8dvi_27739.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dvi_27739/09_2026/8dvi_27739.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dvi_27739/09_2026/8dvi_27739.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dvi_27739/09_2026/8dvi_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-2.2.1-6174/lib/python3.11/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: 5.58, per 1000 atoms: 0.24 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: 2.37 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.75 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: 4.83 Time building geometry restraints manager: 3.12 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=" C3' DT M 14 " pdb=" C2' DT M 14 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DT M 12 " pdb=" C2' DT M 12 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 ... (remaining 24192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 32319 2.49 - 4.98: 452 4.98 - 7.48: 28 7.48 - 9.97: 7 9.97 - 12.46: 1 Bond angle restraints: 32807 Sorted by residual: angle pdb=" N3 DT M 9 " pdb=" C4 DT M 9 " pdb=" O4 DT M 9 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT M 11 " pdb=" C4 DT M 11 " pdb=" O4 DT M 11 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 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=" N3 DT M 14 " pdb=" C4 DT M 14 " pdb=" O4 DT M 14 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT M 17 " pdb=" C4 DT M 17 " pdb=" O4 DT M 17 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 ... (remaining 32802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 14378 35.65 - 71.31: 183 71.31 - 106.96: 10 106.96 - 142.62: 1 142.62 - 178.27: 4 Dihedral angle restraints: 14576 sinusoidal: 6014 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 14573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2633 0.044 - 0.088: 657 0.088 - 0.132: 292 0.132 - 0.176: 49 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: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.550 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 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 : 0.005 0.051 24197 Z= 0.322 Angle : 0.689 12.461 32807 Z= 0.467 Chirality : 0.049 0.220 3647 Planarity : 0.004 0.075 4071 Dihedral : 12.267 178.275 9046 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 are 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/Z covalent geometry : bond 0.00457 / 0.32 (24197) covalent geometry : angle 0.68933 / 0.47 (32807) hydrogen bonds : bond 0.15957 / 11.26 ( 1158) hydrogen bonds : angle 6.57570 / 4.74 ( 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 : 0.914 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: 0.2068 time to fit residues: 229.8917 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 : 0.955 ------------------------------------------------------------------------------- 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... ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 ASN H 195 GLN H 325 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.144507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.116459 restraints weight = 38587.323| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.17 r_work: 0.3316 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24197 Z= 0.142 Angle : 0.569 7.519 32807 Z= 0.313 Chirality : 0.043 0.213 3647 Planarity : 0.004 0.050 4071 Dihedral : 10.260 175.815 3360 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.74 % Allowed : 11.45 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.16), residues: 2898 helix: 1.43 (0.14), residues: 1457 sheet: -0.29 (0.27), residues: 404 loop : -1.17 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 124 TYR 0.023 0.001 TYR H 213 PHE 0.020 0.002 PHE A 417 TRP 0.021 0.001 TRP H 266 HIS 0.012 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (24197) covalent geometry : angle 0.56860 / 0.31 (32807) hydrogen bonds : bond 0.04364 / 2.97 ( 1158) hydrogen bonds : angle 5.30540 / 3.83 ( 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 440 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 396 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.6862 (mmm) cc_final: 0.6580 (mmm) REVERT: A 266 TRP cc_start: 0.7359 (m100) cc_final: 0.7106 (m100) REVERT: A 302 ASN cc_start: 0.7349 (p0) cc_final: 0.6599 (m-40) REVERT: A 369 SER cc_start: 0.6118 (m) cc_final: 0.5740 (p) REVERT: B 48 HIS cc_start: 0.7465 (m90) cc_final: 0.7181 (m90) REVERT: B 253 HIS cc_start: 0.6638 (m-70) cc_final: 0.6434 (m-70) REVERT: B 367 ASN cc_start: 0.7759 (m-40) cc_final: 0.7455 (m-40) REVERT: B 422 GLN cc_start: 0.6819 (mt0) cc_final: 0.6415 (mm-40) REVERT: C 128 MET cc_start: 0.5708 (tpp) cc_final: 0.5367 (mmt) REVERT: C 158 TYR cc_start: 0.6766 (p90) cc_final: 0.6557 (p90) REVERT: D 26 GLU cc_start: 0.8002 (mp0) cc_final: 0.7679 (mm-30) REVERT: E 228 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.7141 (mtp) REVERT: E 274 ARG cc_start: 0.7814 (mtp180) cc_final: 0.7453 (mtp180) REVERT: E 306 THR cc_start: 0.8209 (m) cc_final: 0.7883 (t) REVERT: E 338 GLU cc_start: 0.6627 (mt-10) cc_final: 0.6241 (mp0) REVERT: E 419 MET cc_start: 0.8369 (tpt) cc_final: 0.8068 (tpt) REVERT: F 167 ASN cc_start: 0.5867 (OUTLIER) cc_final: 0.5017 (m-40) REVERT: F 213 ASP cc_start: 0.7325 (m-30) cc_final: 0.7012 (m-30) REVERT: F 399 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7031 (tp40) REVERT: H 141 LYS cc_start: 0.5103 (pttt) cc_final: 0.4880 (ttmt) REVERT: H 161 LYS cc_start: 0.4012 (tmmt) cc_final: 0.3622 (mmtt) REVERT: H 292 MET cc_start: 0.7318 (tpp) cc_final: 0.6330 (tpt) REVERT: H 328 GLN cc_start: 0.7341 (pt0) cc_final: 0.7076 (pt0) outliers start: 44 outliers final: 21 residues processed: 427 average time/residue: 0.1743 time to fit residues: 114.5070 Evaluate side-chains 335 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 311 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 163 LEU 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 328 SER Chi-restraints excluded: chain D residue 109 LYS 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 217 LEU Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 348 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 85 optimal weight: 10.0000 chunk 248 optimal weight: 0.9980 chunk 150 optimal weight: 0.0980 chunk 82 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 ASN A 140 GLN B 114 GLN B 355 GLN ** 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 ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 305 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.144684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.115900 restraints weight = 38354.448| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.16 r_work: 0.3301 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 24197 Z= 0.117 Angle : 0.525 8.688 32807 Z= 0.286 Chirality : 0.042 0.225 3647 Planarity : 0.004 0.049 4071 Dihedral : 10.254 176.657 3352 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.02 % Allowed : 12.37 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.16), residues: 2898 helix: 1.53 (0.14), residues: 1457 sheet: -0.33 (0.27), residues: 407 loop : -1.18 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 124 TYR 0.017 0.001 TYR H 86 PHE 0.024 0.001 PHE C 37 TRP 0.016 0.001 TRP E 20 HIS 0.007 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (24197) covalent geometry : angle 0.52518 / 0.29 (32807) hydrogen bonds : bond 0.03715 / 2.52 ( 1158) hydrogen bonds : angle 4.96828 / 3.58 ( 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 382 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 331 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.6250 (pp20) cc_final: 0.6032 (pp20) REVERT: A 263 MET cc_start: 0.6928 (mmm) cc_final: 0.6625 (mmm) REVERT: A 330 THR cc_start: 0.7554 (m) cc_final: 0.7301 (t) REVERT: A 369 SER cc_start: 0.6231 (m) cc_final: 0.5798 (p) REVERT: A 380 THR cc_start: 0.7383 (p) cc_final: 0.6920 (t) REVERT: B 48 HIS cc_start: 0.7497 (m90) cc_final: 0.7225 (m90) REVERT: B 422 GLN cc_start: 0.6736 (mt0) cc_final: 0.6376 (mm-40) REVERT: C 69 GLU cc_start: 0.7204 (pt0) cc_final: 0.6375 (mm-30) REVERT: C 128 MET cc_start: 0.5686 (tpp) cc_final: 0.5305 (mmt) REVERT: C 188 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7917 (mt-10) REVERT: D 18 LYS cc_start: 0.7838 (ttmm) cc_final: 0.7536 (tttm) REVERT: D 26 GLU cc_start: 0.7949 (mp0) cc_final: 0.7712 (mm-30) REVERT: E 118 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7435 (tm-30) REVERT: E 306 THR cc_start: 0.8207 (m) cc_final: 0.7862 (t) REVERT: E 338 GLU cc_start: 0.6744 (mt-10) cc_final: 0.6239 (mp0) REVERT: F 87 HIS cc_start: 0.7126 (t-90) cc_final: 0.6921 (t-90) REVERT: F 167 ASN cc_start: 0.5997 (OUTLIER) cc_final: 0.4990 (m-40) REVERT: F 213 ASP cc_start: 0.7280 (m-30) cc_final: 0.6953 (m-30) REVERT: F 373 GLU cc_start: 0.7264 (mm-30) cc_final: 0.6811 (mm-30) REVERT: F 399 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7030 (tp40) REVERT: H 141 LYS cc_start: 0.5260 (pttt) cc_final: 0.5032 (ttmt) REVERT: H 292 MET cc_start: 0.7475 (tpp) cc_final: 0.6181 (tpt) REVERT: H 328 GLN cc_start: 0.7280 (pt0) cc_final: 0.6995 (pt0) outliers start: 51 outliers final: 28 residues processed: 367 average time/residue: 0.1574 time to fit residues: 90.3710 Evaluate side-chains 326 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 295 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 404 ILE Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 317 LYS 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 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 119 LEU 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 147 ASP Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 90 LEU 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 282 THR 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: 10.0000 chunk 191 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 chunk 268 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 chunk 289 optimal weight: 5.9990 chunk 288 optimal weight: 20.0000 chunk 128 optimal weight: 8.9990 chunk 285 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 ASN A 140 GLN A 403 GLN A 422 GLN B 116 ASN 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** D 13 GLN ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN D 200 ASN E 114 GLN ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.135952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.107573 restraints weight = 38724.687| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.10 r_work: 0.3162 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 24197 Z= 0.325 Angle : 0.774 11.103 32807 Z= 0.413 Chirality : 0.052 0.328 3647 Planarity : 0.006 0.053 4071 Dihedral : 11.100 175.054 3350 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.41 % Allowed : 13.12 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.15), residues: 2898 helix: 0.83 (0.14), residues: 1449 sheet: -0.43 (0.27), residues: 402 loop : -1.33 (0.17), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 291 TYR 0.020 0.003 TYR D 280 PHE 0.029 0.004 PHE A 417 TRP 0.023 0.003 TRP A 162 HIS 0.010 0.002 HIS H 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00758 / 0.32 (24197) covalent geometry : angle 0.77379 / 0.41 (32807) hydrogen bonds : bond 0.04856 / 3.28 ( 1158) hydrogen bonds : angle 5.35200 / 3.86 ( 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 424 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 338 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7166 (m) cc_final: 0.6900 (t) REVERT: A 118 GLU cc_start: 0.6557 (pp20) cc_final: 0.6238 (pp20) REVERT: A 368 MET cc_start: 0.5919 (ttp) cc_final: 0.5629 (ttp) REVERT: B 48 HIS cc_start: 0.7816 (m90) cc_final: 0.7487 (m90) REVERT: B 248 ASP cc_start: 0.8025 (m-30) cc_final: 0.7741 (m-30) REVERT: B 253 HIS cc_start: 0.6745 (m-70) cc_final: 0.6519 (m-70) REVERT: B 422 GLN cc_start: 0.7412 (mt0) cc_final: 0.7131 (mm-40) REVERT: C 69 GLU cc_start: 0.7321 (pt0) cc_final: 0.6282 (mm-30) REVERT: C 103 MET cc_start: 0.8336 (mmm) cc_final: 0.8129 (mmm) REVERT: C 128 MET cc_start: 0.5810 (tpp) cc_final: 0.5352 (mmt) REVERT: D 26 GLU cc_start: 0.8415 (mp0) cc_final: 0.8168 (mm-30) REVERT: D 108 SER cc_start: 0.8645 (m) cc_final: 0.8410 (t) REVERT: D 130 ASP cc_start: 0.6703 (t0) cc_final: 0.6337 (m-30) REVERT: E 24 ASP cc_start: 0.7101 (m-30) cc_final: 0.6898 (m-30) REVERT: E 48 HIS cc_start: 0.6229 (m90) cc_final: 0.5725 (m170) REVERT: E 79 LYS cc_start: 0.7287 (mtpt) cc_final: 0.6969 (mtmm) REVERT: E 100 GLN cc_start: 0.8359 (tm-30) cc_final: 0.8081 (tm-30) REVERT: E 118 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7749 (pp20) REVERT: E 338 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6322 (mp0) REVERT: F 213 ASP cc_start: 0.7731 (m-30) cc_final: 0.7522 (m-30) REVERT: F 373 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7001 (mm-30) REVERT: H 88 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6147 (mm-30) REVERT: H 136 ILE cc_start: 0.3950 (OUTLIER) cc_final: 0.3671 (mm) REVERT: H 141 LYS cc_start: 0.5312 (pttp) cc_final: 0.5021 (ttmt) REVERT: H 273 ARG cc_start: 0.7692 (mtp85) cc_final: 0.7434 (mtt-85) REVERT: H 281 MET cc_start: 0.8374 (mtp) cc_final: 0.8165 (mtp) REVERT: H 292 MET cc_start: 0.8440 (tpp) cc_final: 0.7975 (tpp) outliers start: 86 outliers final: 61 residues processed: 403 average time/residue: 0.1689 time to fit residues: 106.4520 Evaluate side-chains 369 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 305 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 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 243 ASP Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 350 LEU 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 60 LEU Chi-restraints excluded: chain B residue 61 GLU 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 90 LEU Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 142 LEU 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 152 HIS 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 348 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 90 LEU 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 136 ILE Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 260 PHE 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: 10.0000 chunk 0 optimal weight: 6.9990 chunk 283 optimal weight: 6.9990 chunk 253 optimal weight: 3.9990 chunk 282 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 chunk 266 optimal weight: 20.0000 chunk 281 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 226 optimal weight: 2.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 GLN B 116 ASN ** 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 114 GLN D 200 ASN ** F 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.137274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.108956 restraints weight = 38361.177| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.13 r_work: 0.3186 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 24197 Z= 0.181 Angle : 0.607 10.631 32807 Z= 0.326 Chirality : 0.045 0.275 3647 Planarity : 0.004 0.038 4071 Dihedral : 10.851 179.176 3350 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.85 % Allowed : 14.31 % 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 are not related in a simple way. whole: 0.05 (0.16), residues: 2898 helix: 1.11 (0.14), residues: 1449 sheet: -0.38 (0.27), residues: 393 loop : -1.27 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 124 TYR 0.013 0.002 TYR A 324 PHE 0.020 0.002 PHE C 104 TRP 0.021 0.002 TRP D 162 HIS 0.005 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (24197) covalent geometry : angle 0.60729 / 0.33 (32807) hydrogen bonds : bond 0.03987 / 2.68 ( 1158) hydrogen bonds : angle 5.05530 / 3.63 ( 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 396 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 324 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.6538 (pp20) cc_final: 0.6220 (pp20) REVERT: A 263 MET cc_start: 0.7299 (mmm) cc_final: 0.6994 (mmm) REVERT: B 48 HIS cc_start: 0.7839 (m90) cc_final: 0.7519 (m90) REVERT: B 422 GLN cc_start: 0.7207 (mt0) cc_final: 0.6943 (mm-40) REVERT: C 69 GLU cc_start: 0.7233 (pt0) cc_final: 0.6341 (mm-30) REVERT: C 103 MET cc_start: 0.8323 (mmm) cc_final: 0.8048 (mmm) REVERT: C 128 MET cc_start: 0.5855 (tpp) cc_final: 0.5360 (mmt) REVERT: C 188 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8201 (mt-10) REVERT: D 26 GLU cc_start: 0.8390 (mp0) cc_final: 0.8141 (mm-30) REVERT: D 92 LYS cc_start: 0.8554 (mmmt) cc_final: 0.8348 (mtmt) REVERT: D 108 SER cc_start: 0.8652 (m) cc_final: 0.8427 (t) REVERT: D 130 ASP cc_start: 0.6685 (t0) cc_final: 0.6342 (m-30) REVERT: E 48 HIS cc_start: 0.6308 (m90) cc_final: 0.5852 (m170) REVERT: E 77 ILE cc_start: 0.8025 (pt) cc_final: 0.7355 (mt) REVERT: E 118 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: E 338 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6279 (mp0) REVERT: F 69 GLU cc_start: 0.8026 (mp0) cc_final: 0.7671 (mp0) REVERT: F 124 ARG cc_start: 0.7124 (ptm160) cc_final: 0.6919 (ptp-170) REVERT: F 213 ASP cc_start: 0.7685 (m-30) cc_final: 0.7466 (m-30) REVERT: F 367 ASN cc_start: 0.6568 (p0) cc_final: 0.6127 (m-40) REVERT: H 88 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6138 (mm-30) REVERT: H 141 LYS cc_start: 0.5170 (pttp) cc_final: 0.4906 (ttmt) REVERT: H 273 ARG cc_start: 0.7691 (mtp85) cc_final: 0.7474 (mtt-85) outliers start: 72 outliers final: 50 residues processed: 376 average time/residue: 0.1720 time to fit residues: 100.8966 Evaluate side-chains 351 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 299 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 163 LEU Chi-restraints excluded: chain A residue 166 MET 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 61 GLU Chi-restraints excluded: chain B residue 166 MET 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 367 ASN 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 200 ASN 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 C residue 430 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 282 THR 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 164 SER Chi-restraints excluded: chain E residue 321 ILE 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 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 182 ILE 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: 0.9990 chunk 252 optimal weight: 4.9990 chunk 55 optimal weight: 0.0570 chunk 181 optimal weight: 0.9980 chunk 229 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 235 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 GLN B 253 HIS ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN F 125 ASN F 167 ASN ** 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 = 0.3807 r_free = 0.3807 target = 0.139252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.110944 restraints weight = 38427.221| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.13 r_work: 0.3216 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 24197 Z= 0.116 Angle : 0.546 10.074 32807 Z= 0.293 Chirality : 0.042 0.268 3647 Planarity : 0.004 0.033 4071 Dihedral : 10.616 179.341 3350 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.85 % Allowed : 14.51 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.16), residues: 2898 helix: 1.38 (0.14), residues: 1450 sheet: -0.23 (0.27), residues: 376 loop : -1.19 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 309 TYR 0.019 0.001 TYR H 86 PHE 0.024 0.001 PHE C 104 TRP 0.018 0.001 TRP F 89 HIS 0.011 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (24197) covalent geometry : angle 0.54574 / 0.29 (32807) hydrogen bonds : bond 0.03495 / 2.34 ( 1158) hydrogen bonds : angle 4.82170 / 3.46 ( 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 388 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 316 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 118 GLU cc_start: 0.6512 (pp20) cc_final: 0.6185 (pp20) REVERT: A 259 TYR cc_start: 0.7480 (t80) cc_final: 0.7114 (t80) REVERT: B 48 HIS cc_start: 0.7867 (m90) cc_final: 0.7564 (m90) REVERT: B 312 TYR cc_start: 0.7229 (t80) cc_final: 0.6917 (t80) REVERT: C 69 GLU cc_start: 0.7270 (pt0) cc_final: 0.6375 (mm-30) REVERT: C 103 MET cc_start: 0.8253 (mmm) cc_final: 0.7972 (mmm) REVERT: C 128 MET cc_start: 0.5844 (tpp) cc_final: 0.5277 (mmt) REVERT: C 142 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8056 (mt) REVERT: C 188 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8159 (mt-10) REVERT: D 26 GLU cc_start: 0.8369 (mp0) cc_final: 0.8111 (mm-30) REVERT: E 48 HIS cc_start: 0.6222 (m90) cc_final: 0.5789 (m170) REVERT: E 118 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7816 (tm-30) REVERT: E 274 ARG cc_start: 0.7752 (mtp85) cc_final: 0.7546 (mtm110) REVERT: E 306 THR cc_start: 0.8286 (m) cc_final: 0.7885 (t) REVERT: E 338 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6225 (mp0) REVERT: F 69 GLU cc_start: 0.7985 (mp0) cc_final: 0.7706 (mp0) REVERT: F 213 ASP cc_start: 0.7649 (m-30) cc_final: 0.7421 (m-30) REVERT: F 355 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7992 (mt0) REVERT: F 367 ASN cc_start: 0.6621 (p0) cc_final: 0.6141 (m-40) REVERT: H 88 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.6140 (mm-30) REVERT: H 141 LYS cc_start: 0.5092 (pttp) cc_final: 0.4797 (ttmt) REVERT: H 273 ARG cc_start: 0.7697 (mtp85) cc_final: 0.7494 (mtt-85) REVERT: H 292 MET cc_start: 0.8328 (tpp) cc_final: 0.7520 (tpt) outliers start: 72 outliers final: 46 residues processed: 371 average time/residue: 0.1639 time to fit residues: 95.2601 Evaluate side-chains 341 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 291 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 A residue 404 ILE 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 61 GLU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 201 VAL 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 255 SER Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 363 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 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 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 164 SER Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 251 ASP 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 355 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 182 ILE Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 233 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 270 optimal weight: 1.9990 chunk 246 optimal weight: 9.9990 chunk 286 optimal weight: 0.7980 chunk 256 optimal weight: 5.9990 chunk 269 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN F 13 GLN ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.137695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.109771 restraints weight = 38411.903| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.09 r_work: 0.3204 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24197 Z= 0.151 Angle : 0.569 10.651 32807 Z= 0.304 Chirality : 0.043 0.266 3647 Planarity : 0.004 0.038 4071 Dihedral : 10.636 178.892 3348 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.50 % Allowed : 15.02 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.16), residues: 2898 helix: 1.44 (0.14), residues: 1452 sheet: -0.22 (0.27), residues: 380 loop : -1.23 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 124 TYR 0.023 0.001 TYR D 312 PHE 0.023 0.002 PHE C 104 TRP 0.016 0.001 TRP E 20 HIS 0.005 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (24197) covalent geometry : angle 0.56858 / 0.30 (32807) hydrogen bonds : bond 0.03581 / 2.40 ( 1158) hydrogen bonds : angle 4.82096 / 3.46 ( 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 373 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 310 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 118 GLU cc_start: 0.6455 (pp20) cc_final: 0.6098 (pp20) REVERT: A 259 TYR cc_start: 0.7513 (t80) cc_final: 0.7196 (t80) REVERT: B 48 HIS cc_start: 0.7847 (m90) cc_final: 0.7557 (m90) REVERT: B 248 ASP cc_start: 0.7879 (m-30) cc_final: 0.7626 (m-30) REVERT: C 69 GLU cc_start: 0.7184 (pt0) cc_final: 0.6316 (mm-30) REVERT: C 128 MET cc_start: 0.5822 (tpp) cc_final: 0.5238 (mmt) REVERT: C 188 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8185 (mt-10) REVERT: D 108 SER cc_start: 0.8581 (m) cc_final: 0.8363 (t) REVERT: E 77 ILE cc_start: 0.7974 (pt) cc_final: 0.7314 (mt) REVERT: E 118 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7790 (tm-30) REVERT: E 128 MET cc_start: 0.7449 (mmm) cc_final: 0.7017 (mtp) REVERT: E 274 ARG cc_start: 0.7762 (mtp85) cc_final: 0.7560 (mtm110) REVERT: E 338 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6260 (mp0) REVERT: E 392 GLU cc_start: 0.7230 (pm20) cc_final: 0.6992 (pm20) REVERT: F 69 GLU cc_start: 0.7977 (mp0) cc_final: 0.7669 (mp0) REVERT: F 213 ASP cc_start: 0.7637 (m-30) cc_final: 0.7400 (m-30) REVERT: F 350 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8509 (tt) REVERT: F 367 ASN cc_start: 0.6567 (p0) cc_final: 0.6205 (m-40) REVERT: H 88 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.6111 (mm-30) REVERT: H 141 LYS cc_start: 0.5040 (pttp) cc_final: 0.4693 (ttmt) REVERT: H 197 ARG cc_start: 0.3433 (tpt170) cc_final: 0.3000 (tpt90) REVERT: H 292 MET cc_start: 0.8379 (tpp) cc_final: 0.7559 (tpt) outliers start: 63 outliers final: 49 residues processed: 358 average time/residue: 0.1758 time to fit residues: 97.8125 Evaluate side-chains 348 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 296 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 163 LEU 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 258 GLU Chi-restraints excluded: chain A residue 350 LEU 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 61 GLU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 201 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 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 C residue 363 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 201 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 304 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 164 SER 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 350 LEU 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 182 ILE Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 203 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 252 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 166 optimal weight: 8.9990 chunk 47 optimal weight: 0.0000 chunk 247 optimal weight: 4.9990 chunk 143 optimal weight: 0.7980 chunk 237 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 HIS ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.137811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.109230 restraints weight = 38413.913| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.12 r_work: 0.3194 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24197 Z= 0.152 Angle : 0.573 9.946 32807 Z= 0.306 Chirality : 0.043 0.260 3647 Planarity : 0.004 0.039 4071 Dihedral : 10.639 178.431 3348 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.46 % Allowed : 15.38 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.16), residues: 2898 helix: 1.44 (0.14), residues: 1453 sheet: -0.18 (0.28), residues: 376 loop : -1.26 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 124 TYR 0.029 0.001 TYR D 312 PHE 0.024 0.002 PHE C 104 TRP 0.015 0.001 TRP E 20 HIS 0.005 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (24197) covalent geometry : angle 0.57299 / 0.31 (32807) hydrogen bonds : bond 0.03542 / 2.37 ( 1158) hydrogen bonds : angle 4.80414 / 3.45 ( 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 369 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 307 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.6531 (pp20) cc_final: 0.6176 (pp20) REVERT: A 203 LYS cc_start: 0.7892 (mttt) cc_final: 0.7255 (mtmm) REVERT: B 48 HIS cc_start: 0.7884 (m90) cc_final: 0.7604 (m90) REVERT: B 158 TYR cc_start: 0.8112 (p90) cc_final: 0.7724 (p90) REVERT: B 248 ASP cc_start: 0.7962 (m-30) cc_final: 0.7688 (m-30) REVERT: C 69 GLU cc_start: 0.7180 (pt0) cc_final: 0.6300 (mm-30) REVERT: C 128 MET cc_start: 0.5789 (tpp) cc_final: 0.5376 (mmt) REVERT: C 142 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8128 (mt) REVERT: C 188 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8219 (mt-10) REVERT: D 108 SER cc_start: 0.8588 (m) cc_final: 0.8380 (t) REVERT: E 77 ILE cc_start: 0.7980 (pt) cc_final: 0.7343 (mt) REVERT: E 118 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7815 (tm-30) REVERT: E 128 MET cc_start: 0.7351 (mmm) cc_final: 0.7047 (mtp) REVERT: E 338 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6266 (mp0) REVERT: F 69 GLU cc_start: 0.8025 (mp0) cc_final: 0.7740 (mp0) REVERT: F 213 ASP cc_start: 0.7685 (m-30) cc_final: 0.7450 (m-30) REVERT: F 337 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7086 (mt-10) REVERT: F 367 ASN cc_start: 0.6667 (p0) cc_final: 0.6308 (m-40) REVERT: H 88 GLU cc_start: 0.6566 (OUTLIER) cc_final: 0.6127 (mm-30) REVERT: H 141 LYS cc_start: 0.5090 (pttp) cc_final: 0.4725 (ttmt) REVERT: H 292 MET cc_start: 0.8411 (tpp) cc_final: 0.7614 (tpt) outliers start: 62 outliers final: 52 residues processed: 353 average time/residue: 0.1771 time to fit residues: 96.7868 Evaluate side-chains 348 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 292 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 98 VAL Chi-restraints excluded: chain A residue 163 LEU 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 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 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 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 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 363 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 217 LEU Chi-restraints excluded: chain D residue 282 THR 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 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 164 SER 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 337 GLU Chi-restraints excluded: chain F residue 355 GLN 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 182 ILE Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 116 optimal weight: 7.9990 chunk 207 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 161 optimal weight: 0.2980 chunk 74 optimal weight: 0.8980 chunk 276 optimal weight: 10.0000 chunk 121 optimal weight: 0.7980 chunk 179 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS B 200 ASN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN F 399 GLN ** 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 = 0.3799 r_free = 0.3799 target = 0.138591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.110648 restraints weight = 38515.732| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.08 r_work: 0.3217 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24197 Z= 0.126 Angle : 0.545 9.083 32807 Z= 0.292 Chirality : 0.042 0.252 3647 Planarity : 0.004 0.040 4071 Dihedral : 10.578 177.849 3348 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.58 % Allowed : 15.14 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.16), residues: 2898 helix: 1.54 (0.14), residues: 1453 sheet: -0.04 (0.28), residues: 369 loop : -1.26 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 124 TYR 0.037 0.001 TYR D 312 PHE 0.026 0.001 PHE C 104 TRP 0.021 0.001 TRP F 89 HIS 0.005 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (24197) covalent geometry : angle 0.54530 / 0.29 (32807) hydrogen bonds : bond 0.03332 / 2.24 ( 1158) hydrogen bonds : angle 4.71897 / 3.39 ( 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 375 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 310 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.6465 (pp20) cc_final: 0.6111 (pp20) REVERT: A 203 LYS cc_start: 0.7886 (mttt) cc_final: 0.7267 (mtmm) REVERT: A 259 TYR cc_start: 0.7528 (t80) cc_final: 0.6991 (t80) REVERT: B 48 HIS cc_start: 0.7843 (m90) cc_final: 0.7596 (m90) REVERT: B 248 ASP cc_start: 0.7980 (m-30) cc_final: 0.7684 (m-30) REVERT: B 312 TYR cc_start: 0.7230 (t80) cc_final: 0.6926 (t80) REVERT: C 69 GLU cc_start: 0.7235 (pt0) cc_final: 0.6370 (mm-30) REVERT: C 128 MET cc_start: 0.5752 (tpp) cc_final: 0.5328 (mmt) REVERT: C 142 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8140 (mt) REVERT: C 188 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8184 (mt-10) REVERT: D 108 SER cc_start: 0.8583 (m) cc_final: 0.8373 (t) REVERT: E 74 LYS cc_start: 0.7485 (ttmm) cc_final: 0.7285 (ttmm) REVERT: E 77 ILE cc_start: 0.7964 (pt) cc_final: 0.7377 (mt) REVERT: E 118 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: E 269 LYS cc_start: 0.8300 (mttm) cc_final: 0.7881 (mmtm) REVERT: E 306 THR cc_start: 0.8276 (m) cc_final: 0.7837 (t) REVERT: E 338 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6191 (mp0) REVERT: F 69 GLU cc_start: 0.7943 (mp0) cc_final: 0.7732 (mp0) REVERT: F 213 ASP cc_start: 0.7628 (m-30) cc_final: 0.7386 (m-30) REVERT: F 274 ARG cc_start: 0.7874 (mtp85) cc_final: 0.7624 (mtp-110) REVERT: F 337 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7123 (mt-10) REVERT: F 350 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8503 (tt) REVERT: F 367 ASN cc_start: 0.6688 (p0) cc_final: 0.6301 (m-40) REVERT: H 88 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.6116 (mm-30) REVERT: H 141 LYS cc_start: 0.5035 (pttp) cc_final: 0.4660 (ttmt) REVERT: H 292 MET cc_start: 0.8395 (tpp) cc_final: 0.7625 (tpt) outliers start: 65 outliers final: 51 residues processed: 358 average time/residue: 0.1709 time to fit residues: 95.9729 Evaluate side-chains 355 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 299 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 189 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 350 LEU 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 61 GLU Chi-restraints excluded: chain B residue 66 THR 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 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 C residue 363 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 201 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 282 THR 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 164 SER 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 326 GLU Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 355 GLN 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 182 ILE Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 242 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 179 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 208 optimal weight: 7.9990 chunk 241 optimal weight: 0.8980 chunk 135 optimal weight: 10.0000 chunk 184 optimal weight: 0.0170 overall best weight: 1.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 ASN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.139074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.110952 restraints weight = 38462.253| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.11 r_work: 0.3230 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4443 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= 0.117 Angle : 0.539 9.602 32807 Z= 0.289 Chirality : 0.041 0.248 3647 Planarity : 0.003 0.040 4071 Dihedral : 10.530 177.766 3348 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.98 % Allowed : 15.89 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.16), residues: 2898 helix: 1.61 (0.14), residues: 1452 sheet: -0.03 (0.28), residues: 378 loop : -1.29 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 124 TYR 0.040 0.001 TYR D 312 PHE 0.025 0.001 PHE C 104 TRP 0.018 0.001 TRP F 89 HIS 0.005 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (24197) covalent geometry : angle 0.53910 / 0.29 (32807) hydrogen bonds : bond 0.03225 / 2.16 ( 1158) hydrogen bonds : angle 4.66580 / 3.35 ( 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 358 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 308 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 LYS cc_start: 0.7918 (mttt) cc_final: 0.7318 (mtmm) REVERT: A 259 TYR cc_start: 0.7505 (t80) cc_final: 0.6909 (t80) REVERT: B 48 HIS cc_start: 0.7858 (m90) cc_final: 0.7619 (m90) REVERT: B 248 ASP cc_start: 0.7975 (m-30) cc_final: 0.7682 (m-30) REVERT: B 312 TYR cc_start: 0.7248 (t80) cc_final: 0.6973 (t80) REVERT: C 69 GLU cc_start: 0.7217 (pt0) cc_final: 0.6341 (mm-30) REVERT: C 128 MET cc_start: 0.5726 (tpp) cc_final: 0.5281 (mmt) REVERT: C 142 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8146 (mt) REVERT: C 188 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8189 (mt-10) REVERT: D 293 LEU cc_start: 0.7750 (tp) cc_final: 0.7414 (tp) REVERT: D 298 LYS cc_start: 0.7301 (ttpt) cc_final: 0.6569 (ptmt) REVERT: E 77 ILE cc_start: 0.7958 (pt) cc_final: 0.7403 (mt) REVERT: E 118 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7787 (tm-30) REVERT: E 269 LYS cc_start: 0.8283 (mttm) cc_final: 0.7852 (mmtm) REVERT: E 306 THR cc_start: 0.8279 (m) cc_final: 0.7833 (t) REVERT: E 338 GLU cc_start: 0.6896 (mt-10) cc_final: 0.6175 (mp0) REVERT: F 213 ASP cc_start: 0.7665 (m-30) cc_final: 0.7427 (m-30) REVERT: F 274 ARG cc_start: 0.7893 (mtp85) cc_final: 0.7652 (mtp-110) REVERT: F 337 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7106 (mt-10) REVERT: F 350 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8514 (tt) REVERT: F 367 ASN cc_start: 0.6696 (p0) cc_final: 0.6306 (m-40) REVERT: H 49 LYS cc_start: 0.1135 (mttt) cc_final: 0.0740 (ptpt) REVERT: H 88 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.6144 (mm-30) REVERT: H 141 LYS cc_start: 0.5050 (pttp) cc_final: 0.4690 (ttmt) REVERT: H 292 MET cc_start: 0.8374 (tpp) cc_final: 0.7643 (tpt) outliers start: 50 outliers final: 42 residues processed: 346 average time/residue: 0.1733 time to fit residues: 93.5060 Evaluate side-chains 343 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 296 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 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 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 142 LEU 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 363 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 282 THR 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 164 SER 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 337 GLU Chi-restraints excluded: chain F residue 350 LEU 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 182 ILE Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 52 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 142 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 273 optimal weight: 2.9990 chunk 226 optimal weight: 8.9990 chunk 251 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 17 optimal weight: 0.0980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 ASN F 253 HIS ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 325 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.140029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.112175 restraints weight = 38326.335| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.08 r_work: 0.3244 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24197 Z= 0.108 Angle : 0.531 8.924 32807 Z= 0.285 Chirality : 0.041 0.242 3647 Planarity : 0.003 0.040 4071 Dihedral : 10.474 177.639 3348 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.82 % Allowed : 15.89 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.16), residues: 2898 helix: 1.69 (0.14), residues: 1449 sheet: 0.06 (0.28), residues: 374 loop : -1.30 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 274 TYR 0.024 0.001 TYR D 312 PHE 0.026 0.001 PHE C 104 TRP 0.019 0.001 TRP F 89 HIS 0.006 0.001 HIS F 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (24197) covalent geometry : angle 0.53140 / 0.28 (32807) hydrogen bonds : bond 0.03096 / 2.07 ( 1158) hydrogen bonds : angle 4.62417 / 3.31 ( 3303) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6337.41 seconds wall clock time: 109 minutes 35.27 seconds (6575.27 seconds total)