Starting phenix.real_space_refine on Sat Jul 4 21:19:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dvf_27737/07_2026/8dvf_27737.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dvf_27737/07_2026/8dvf_27737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dvf_27737/07_2026/8dvf_27737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dvf_27737/07_2026/8dvf_27737.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8dvf_27737/07_2026/8dvf_27737.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dvf_27737/07_2026/8dvf_27737.cif" model { file = "/net/cci-nas-00/data/ceres_data/8dvf_27737/07_2026/8dvf_27737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dvf_27737/07_2026/8dvf_27737.cif" } resolution = 3.3 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 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 5.31, per 1000 atoms: 0.22 Number of scatterers: 23693 At special positions: 0 Unit cell: (131.652, 130.824, 141.588, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 132 16.00 P 32 15.00 Mg 5 11.99 O 4586 8.00 N 3943 7.00 C 14995 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 759.3 milliseconds 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 53.9% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 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: 3.708A 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: 3.728A 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: 3.543A 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: 3.843A 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: 3.608A 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: 4.152A 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 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: 3.593A 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: 3.588A 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: 3.843A 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: 3.705A 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: 3.661A pdb=" N ARG H 14 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.644A 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 97 removed outlier: 3.858A pdb=" N GLU H 88 " --> pdb=" O ASP H 84 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG H 94 " --> pdb=" O ILE H 90 " (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: 3.607A 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: 3.605A 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: 3.853A 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 removed outlier: 3.513A pdb=" N ARG H 335 " --> pdb=" O MET H 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 153 removed outlier: 6.564A pdb=" N VAL B 221 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 7.801A 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: 6.442A 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: 3.936A 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: 6.512A pdb=" N MET A 384 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.772A 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: 7.765A pdb=" N VAL A 387 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.401A 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: 7.742A 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: 7.760A pdb=" N ALA A 354 " --> pdb=" O ASN A 193 " (cutoff:3.500A) removed outlier: 5.954A 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: 6.470A 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: 7.739A 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: 6.615A pdb=" N VAL C 221 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LYS C 278 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.242A 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: 7.639A 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: 3.526A 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: 6.113A 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: 3.522A 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: 8.044A pdb=" N LEU E 385 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 6.324A 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: 6.346A pdb=" N ASN D 193 " --> pdb=" O THR D 352 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ALA D 354 " --> pdb=" O ASN D 193 " (cutoff:3.500A) removed outlier: 5.929A 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: 6.540A 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: 6.324A 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: 6.438A 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: 3.509A pdb=" N ALA H 327 " --> pdb=" O VAL H 291 " (cutoff:3.500A) 1158 hydrogen bonds defined for protein. 3303 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.93 Time building geometry restraints manager: 2.58 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: 7550 1.35 - 1.50: 6427 1.50 - 1.65: 9991 1.65 - 1.80: 110 1.80 - 1.95: 119 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 1.47e+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 1.25e+01 bond pdb=" N ILE A 321 " pdb=" CA ILE A 321 " ideal model delta sigma weight residual 1.452 1.494 -0.042 1.18e-02 7.18e+03 1.25e+01 bond pdb=" N VAL E 19 " pdb=" CA VAL E 19 " ideal model delta sigma weight residual 1.452 1.492 -0.040 1.18e-02 7.18e+03 1.14e+01 bond pdb=" N VAL A 323 " pdb=" CA VAL A 323 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.08e-02 8.57e+03 1.11e+01 ... (remaining 24192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 32325 2.51 - 5.01: 446 5.01 - 7.52: 27 7.52 - 10.03: 8 10.03 - 12.53: 1 Bond angle restraints: 32807 Sorted by residual: angle pdb=" N ILE A 321 " pdb=" CA ILE A 321 " pdb=" C ILE A 321 " ideal model delta sigma weight residual 112.96 108.30 4.66 1.00e+00 1.00e+00 2.17e+01 angle pdb=" PB AGS C 501 " pdb=" O3B AGS C 501 " pdb=" PG AGS C 501 " ideal model delta sigma weight residual 120.12 132.65 -12.53 3.00e+00 1.11e-01 1.75e+01 angle pdb=" N3 DT M 15 " pdb=" C4 DT M 15 " pdb=" O4 DT M 15 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT M 9 " pdb=" C4 DT M 9 " pdb=" O4 DT M 9 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT M 6 " pdb=" C4 DT M 6 " pdb=" O4 DT M 6 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 ... (remaining 32802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 14378 35.65 - 71.31: 184 71.31 - 106.96: 9 106.96 - 142.61: 1 142.61 - 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 -67.73 106.44 -174.17 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 - 0.047: 2710 0.047 - 0.093: 634 0.093 - 0.140: 246 0.140 - 0.186: 46 0.186 - 0.233: 11 Chirality restraints: 3647 Sorted by residual: chirality pdb=" CA ILE B 111 " pdb=" N ILE B 111 " pdb=" C ILE B 111 " pdb=" CB ILE B 111 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.35e+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 1.21e+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 1.20e+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 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 266 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 266 " 0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP H 266 " -0.005 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 3.33e-02 1.11e+01 pdb=" C GLU A 373 " 0.058 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 2.29e-02 5.23e+00 pdb=" C SER B 145 " 0.040 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: 114 2.47 - 3.08: 16485 3.08 - 3.68: 36383 3.68 - 4.29: 55317 4.29 - 4.90: 90427 Nonbonded interactions: 198726 Sorted by model distance: nonbonded pdb=" O1B AGS C 501 " pdb="MG MG C 502 " model vdw 1.862 2.170 nonbonded pdb=" O3B AGS B 501 " pdb="MG MG B 502 " model vdw 1.973 2.170 nonbonded pdb=" OE2 GLU B 227 " pdb="MG MG B 502 " model vdw 1.980 2.170 nonbonded pdb=" O2G AGS E 501 " pdb="MG MG E 502 " model vdw 1.984 2.170 nonbonded pdb=" O2B AGS F 501 " pdb="MG MG F 502 " model vdw 1.993 2.170 ... (remaining 198721 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: 2.260 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: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 20.160 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24197 Z= 0.316 Angle : 0.689 12.535 32807 Z= 0.464 Chirality : 0.049 0.233 3647 Planarity : 0.004 0.075 4071 Dihedral : 12.290 178.268 9046 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.78 % Allowed : 7.13 % Favored : 91.08 % 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: 0.22 (0.16), residues: 2898 helix: 1.28 (0.14), residues: 1436 sheet: -0.35 (0.27), residues: 407 loop : -1.21 (0.18), residues: 1055 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 0.00448 / 0.32 (24197) covalent geometry : angle 0.68897 / 0.46 (32807) hydrogen bonds : bond 0.15940 / 11.34 ( 1158) hydrogen bonds : angle 6.57971 / 4.73 ( 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 809 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 764 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 TYR cc_start: 0.7889 (m-80) cc_final: 0.7365 (m-80) REVERT: A 47 TYR cc_start: 0.6915 (m-10) cc_final: 0.6704 (m-10) REVERT: A 104 PHE cc_start: 0.7783 (t80) cc_final: 0.7431 (t80) REVERT: A 150 VAL cc_start: 0.8809 (t) cc_final: 0.8597 (m) REVERT: A 164 SER cc_start: 0.8518 (m) cc_final: 0.8224 (t) REVERT: A 228 MET cc_start: 0.6399 (mtp) cc_final: 0.5939 (mtp) REVERT: A 292 SER cc_start: 0.7262 (p) cc_final: 0.7024 (t) REVERT: A 333 LYS cc_start: 0.5793 (OUTLIER) cc_final: 0.5552 (tttp) REVERT: B 66 THR cc_start: 0.6091 (p) cc_final: 0.5696 (m) REVERT: B 150 VAL cc_start: 0.8593 (t) cc_final: 0.8332 (p) REVERT: B 299 LEU cc_start: 0.8502 (mt) cc_final: 0.8068 (mt) REVERT: B 312 TYR cc_start: 0.5027 (t80) cc_final: 0.4790 (t80) REVERT: C 85 GLU cc_start: 0.5980 (mm-30) cc_final: 0.5749 (mm-30) REVERT: C 150 VAL cc_start: 0.7503 (p) cc_final: 0.7095 (p) REVERT: C 157 ASP cc_start: 0.7634 (m-30) cc_final: 0.7303 (m-30) REVERT: C 263 MET cc_start: 0.8289 (mmm) cc_final: 0.8036 (mmp) REVERT: C 312 TYR cc_start: 0.4659 (t80) cc_final: 0.4421 (t80) REVERT: C 324 TYR cc_start: 0.7816 (m-80) cc_final: 0.7609 (m-80) REVERT: D 103 MET cc_start: 0.7495 (mmm) cc_final: 0.7255 (mtp) REVERT: D 293 LEU cc_start: 0.8466 (tp) cc_final: 0.8196 (tt) REVERT: D 384 MET cc_start: 0.8386 (mtm) cc_final: 0.8127 (mtm) REVERT: E 344 VAL cc_start: 0.7064 (p) cc_final: 0.6844 (m) REVERT: E 392 GLU cc_start: 0.6637 (mt-10) cc_final: 0.6217 (mm-30) REVERT: E 414 TRP cc_start: 0.7134 (m-90) cc_final: 0.6525 (m-90) REVERT: F 233 CYS cc_start: 0.7658 (m) cc_final: 0.7419 (m) REVERT: F 279 GLN cc_start: 0.7377 (tt0) cc_final: 0.7072 (tt0) REVERT: F 303 PHE cc_start: 0.8055 (t80) cc_final: 0.7852 (t80) REVERT: F 311 ASP cc_start: 0.7476 (t0) cc_final: 0.6696 (p0) REVERT: F 399 GLN cc_start: 0.6490 (OUTLIER) cc_final: 0.5586 (mt0) REVERT: F 418 LEU cc_start: 0.6114 (OUTLIER) cc_final: 0.5884 (tt) REVERT: F 430 GLU cc_start: 0.5715 (mt-10) cc_final: 0.5416 (tt0) REVERT: H 35 PHE cc_start: 0.4147 (p90) cc_final: 0.3923 (p90) REVERT: H 80 GLU cc_start: 0.5633 (mm-30) cc_final: 0.4519 (pt0) REVERT: H 88 GLU cc_start: 0.6975 (pt0) cc_final: 0.6582 (pm20) REVERT: H 89 TYR cc_start: 0.6084 (t80) cc_final: 0.5848 (t80) REVERT: H 213 TYR cc_start: 0.4202 (p90) cc_final: 0.3856 (p90) REVERT: H 225 VAL cc_start: 0.5885 (t) cc_final: 0.5645 (t) REVERT: H 234 GLU cc_start: 0.5461 (mt-10) cc_final: 0.4966 (mt-10) REVERT: H 244 ASN cc_start: 0.5804 (m-40) cc_final: 0.5280 (t0) REVERT: H 254 ASP cc_start: 0.4001 (t0) cc_final: 0.3725 (t70) REVERT: H 264 ARG cc_start: 0.5244 (ptt180) cc_final: 0.4731 (ptt180) REVERT: H 270 ASN cc_start: 0.6320 (t0) cc_final: 0.6112 (t0) REVERT: H 276 ASP cc_start: 0.6781 (m-30) cc_final: 0.6503 (m-30) REVERT: H 278 ILE cc_start: 0.6903 (pp) cc_final: 0.6483 (mm) REVERT: H 281 MET cc_start: 0.6844 (mmt) cc_final: 0.6395 (mmm) REVERT: H 289 GLU cc_start: 0.6628 (mm-30) cc_final: 0.5611 (mm-30) REVERT: H 293 PHE cc_start: 0.6403 (m-80) cc_final: 0.5795 (m-80) REVERT: H 322 MET cc_start: 0.6755 (mtm) cc_final: 0.6542 (mtm) outliers start: 45 outliers final: 7 residues processed: 794 average time/residue: 0.1682 time to fit residues: 200.0972 Evaluate side-chains 394 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 384 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain H residue 334 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 GLN A 116 ASN A 403 GLN B 200 ASN B 355 GLN B 399 GLN C 8 HIS ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN D 167 ASN E 57 ASN E 114 GLN F 398 GLN H 195 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.151939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.127262 restraints weight = 39577.584| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.13 r_work: 0.3481 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 24197 Z= 0.162 Angle : 0.603 6.838 32807 Z= 0.328 Chirality : 0.044 0.190 3647 Planarity : 0.004 0.068 4071 Dihedral : 10.339 172.184 3363 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.42 % Allowed : 12.13 % Favored : 85.45 % 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: 0.28 (0.16), residues: 2898 helix: 1.32 (0.14), residues: 1456 sheet: -0.44 (0.26), residues: 421 loop : -1.14 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 124 TYR 0.022 0.002 TYR H 13 PHE 0.014 0.002 PHE H 11 TRP 0.022 0.001 TRP H 266 HIS 0.010 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (24197) covalent geometry : angle 0.60296 / 0.33 (32807) hydrogen bonds : bond 0.04343 / 2.95 ( 1158) hydrogen bonds : angle 5.24716 / 3.76 ( 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 465 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 404 time to evaluate : 0.642 Fit side-chains REVERT: A 19 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.8211 (t) REVERT: A 22 TYR cc_start: 0.7949 (m-80) cc_final: 0.7430 (m-80) REVERT: A 47 TYR cc_start: 0.7332 (m-10) cc_final: 0.7110 (m-10) REVERT: A 73 VAL cc_start: 0.7596 (t) cc_final: 0.7391 (m) REVERT: A 419 MET cc_start: 0.7443 (tpp) cc_final: 0.6893 (tpt) REVERT: C 85 GLU cc_start: 0.6728 (mm-30) cc_final: 0.6439 (mm-30) REVERT: C 157 ASP cc_start: 0.7742 (m-30) cc_final: 0.7450 (m-30) REVERT: D 103 MET cc_start: 0.7205 (mmm) cc_final: 0.6974 (mtp) REVERT: D 264 GLU cc_start: 0.6665 (mm-30) cc_final: 0.6445 (mm-30) REVERT: E 228 MET cc_start: 0.7578 (mtm) cc_final: 0.7248 (ptm) REVERT: E 392 GLU cc_start: 0.6848 (mt-10) cc_final: 0.6237 (mm-30) REVERT: E 413 LYS cc_start: 0.7134 (tppt) cc_final: 0.6880 (tppp) REVERT: E 414 TRP cc_start: 0.7246 (m-90) cc_final: 0.6641 (m-90) REVERT: F 311 ASP cc_start: 0.7418 (t0) cc_final: 0.6774 (p0) REVERT: F 418 LEU cc_start: 0.6073 (OUTLIER) cc_final: 0.5773 (tt) REVERT: H 80 GLU cc_start: 0.7662 (mm-30) cc_final: 0.5916 (pt0) REVERT: H 244 ASN cc_start: 0.6529 (m-40) cc_final: 0.6152 (t0) REVERT: H 264 ARG cc_start: 0.6771 (ptt180) cc_final: 0.6076 (ptt180) REVERT: H 278 ILE cc_start: 0.8397 (pp) cc_final: 0.7872 (mm) REVERT: H 281 MET cc_start: 0.7656 (mmt) cc_final: 0.7125 (mmm) outliers start: 61 outliers final: 33 residues processed: 447 average time/residue: 0.1523 time to fit residues: 106.7448 Evaluate side-chains 355 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 320 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 285 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 85 optimal weight: 8.9990 chunk 248 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 178 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 244 optimal weight: 2.9990 chunk 6 optimal weight: 0.0670 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 GLN A 327 ASN B 200 ASN B 355 GLN C 35 ASN C 125 ASN D 114 GLN D 167 ASN D 399 GLN F 57 ASN H 328 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.150360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.125121 restraints weight = 39567.287| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.17 r_work: 0.3455 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24197 Z= 0.144 Angle : 0.560 7.705 32807 Z= 0.304 Chirality : 0.043 0.209 3647 Planarity : 0.004 0.083 4071 Dihedral : 10.324 170.032 3356 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.58 % Allowed : 13.36 % Favored : 84.07 % 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: 0.29 (0.16), residues: 2898 helix: 1.33 (0.14), residues: 1457 sheet: -0.32 (0.27), residues: 404 loop : -1.21 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 94 TYR 0.025 0.001 TYR F 15 PHE 0.014 0.002 PHE A 104 TRP 0.016 0.001 TRP A 361 HIS 0.005 0.001 HIS H 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (24197) covalent geometry : angle 0.55977 / 0.30 (32807) hydrogen bonds : bond 0.03829 / 2.60 ( 1158) hydrogen bonds : angle 4.92560 / 3.54 ( 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 421 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 356 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 19 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8127 (t) REVERT: A 38 LYS cc_start: 0.7530 (mttm) cc_final: 0.6973 (ttmm) REVERT: C 85 GLU cc_start: 0.6944 (mm-30) cc_final: 0.6695 (mm-30) REVERT: C 157 ASP cc_start: 0.7806 (m-30) cc_final: 0.7511 (m-30) REVERT: D 103 MET cc_start: 0.7176 (mmm) cc_final: 0.6957 (mtp) REVERT: E 392 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6403 (mm-30) REVERT: E 414 TRP cc_start: 0.7280 (m-90) cc_final: 0.6620 (m-90) REVERT: F 311 ASP cc_start: 0.7578 (t0) cc_final: 0.6616 (p0) REVERT: F 399 GLN cc_start: 0.6767 (OUTLIER) cc_final: 0.6330 (tp40) REVERT: F 418 LEU cc_start: 0.5969 (OUTLIER) cc_final: 0.5582 (tt) REVERT: H 80 GLU cc_start: 0.7718 (mm-30) cc_final: 0.6396 (tt0) REVERT: H 213 TYR cc_start: 0.4547 (p90) cc_final: 0.4217 (p90) REVERT: H 244 ASN cc_start: 0.6601 (m-40) cc_final: 0.6344 (t0) REVERT: H 278 ILE cc_start: 0.8322 (pp) cc_final: 0.7985 (mm) REVERT: H 281 MET cc_start: 0.7687 (mmt) cc_final: 0.7085 (mmm) outliers start: 65 outliers final: 44 residues processed: 401 average time/residue: 0.1484 time to fit residues: 93.5186 Evaluate side-chains 357 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 310 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 175 LYS Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 285 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 194 optimal weight: 9.9990 chunk 236 optimal weight: 9.9990 chunk 191 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 268 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 289 optimal weight: 10.0000 chunk 288 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 285 optimal weight: 0.7980 chunk 132 optimal weight: 8.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 114 GLN D 167 ASN F 216 GLN H 325 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.149050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.124091 restraints weight = 39415.691| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.14 r_work: 0.3431 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24197 Z= 0.149 Angle : 0.550 7.239 32807 Z= 0.297 Chirality : 0.043 0.229 3647 Planarity : 0.004 0.039 4071 Dihedral : 10.396 169.750 3354 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.21 % Allowed : 13.71 % Favored : 83.08 % 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: 0.25 (0.16), residues: 2898 helix: 1.33 (0.14), residues: 1449 sheet: -0.31 (0.27), residues: 399 loop : -1.28 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 124 TYR 0.015 0.001 TYR H 185 PHE 0.015 0.002 PHE E 16 TRP 0.011 0.001 TRP F 89 HIS 0.004 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (24197) covalent geometry : angle 0.55028 / 0.30 (32807) hydrogen bonds : bond 0.03650 / 2.48 ( 1158) hydrogen bonds : angle 4.83414 / 3.47 ( 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: 81 poor density : 343 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7559 (mttm) cc_final: 0.7051 (ttmm) REVERT: C 85 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6809 (mm-30) REVERT: C 118 GLU cc_start: 0.6304 (tm-30) cc_final: 0.5478 (tt0) REVERT: C 157 ASP cc_start: 0.7895 (m-30) cc_final: 0.7648 (m-30) REVERT: D 134 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7779 (mt) REVERT: D 406 SER cc_start: 0.7688 (t) cc_final: 0.7440 (p) REVERT: E 392 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6503 (mm-30) REVERT: E 414 TRP cc_start: 0.7279 (m-90) cc_final: 0.6150 (m-90) REVERT: F 321 ILE cc_start: 0.6994 (mt) cc_final: 0.6778 (mt) REVERT: F 326 GLU cc_start: 0.5871 (mp0) cc_final: 0.5575 (mp0) REVERT: F 399 GLN cc_start: 0.6690 (OUTLIER) cc_final: 0.6277 (tp40) REVERT: F 418 LEU cc_start: 0.6099 (OUTLIER) cc_final: 0.5655 (tt) REVERT: H 80 GLU cc_start: 0.7821 (mm-30) cc_final: 0.6625 (tm-30) REVERT: H 213 TYR cc_start: 0.4377 (p90) cc_final: 0.4039 (p90) REVERT: H 244 ASN cc_start: 0.6728 (m-40) cc_final: 0.6403 (t0) REVERT: H 264 ARG cc_start: 0.6703 (ptt180) cc_final: 0.6478 (ptt180) REVERT: H 278 ILE cc_start: 0.8303 (pp) cc_final: 0.8038 (mm) REVERT: H 281 MET cc_start: 0.7683 (mmt) cc_final: 0.7132 (mmm) REVERT: H 282 THR cc_start: 0.7920 (m) cc_final: 0.7537 (p) outliers start: 81 outliers final: 52 residues processed: 404 average time/residue: 0.1415 time to fit residues: 90.3880 Evaluate side-chains 362 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 307 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 175 LYS Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 308 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 283 optimal weight: 20.0000 chunk 253 optimal weight: 9.9990 chunk 282 optimal weight: 0.9990 chunk 134 optimal weight: 9.9990 chunk 266 optimal weight: 8.9990 chunk 281 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 226 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 ASN B 200 ASN C 114 GLN C 398 GLN D 114 GLN D 167 ASN ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.144392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.119503 restraints weight = 39629.697| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.09 r_work: 0.3359 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 24197 Z= 0.235 Angle : 0.669 9.085 32807 Z= 0.356 Chirality : 0.047 0.234 3647 Planarity : 0.005 0.046 4071 Dihedral : 10.803 163.022 3354 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.92 % Allowed : 14.07 % Favored : 82.01 % 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: -0.27 (0.15), residues: 2898 helix: 0.90 (0.14), residues: 1447 sheet: -0.59 (0.26), residues: 397 loop : -1.49 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 87 TYR 0.037 0.002 TYR H 86 PHE 0.023 0.003 PHE H 81 TRP 0.017 0.002 TRP A 162 HIS 0.019 0.002 HIS D 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.24 (24197) covalent geometry : angle 0.66851 / 0.36 (32807) hydrogen bonds : bond 0.04325 / 2.93 ( 1158) hydrogen bonds : angle 5.09099 / 3.65 ( 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 437 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 338 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7567 (mttm) cc_final: 0.7113 (ttmm) REVERT: A 69 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6380 (mp0) REVERT: A 74 LYS cc_start: 0.6857 (tptp) cc_final: 0.6398 (ttpp) REVERT: A 345 GLU cc_start: 0.8022 (tp30) cc_final: 0.7795 (tp30) REVERT: A 355 GLN cc_start: 0.7516 (tp40) cc_final: 0.6511 (mm-40) REVERT: C 47 TYR cc_start: 0.5643 (OUTLIER) cc_final: 0.4680 (m-80) REVERT: C 175 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7974 (tptt) REVERT: C 431 ILE cc_start: 0.7044 (mm) cc_final: 0.6833 (mt) REVERT: D 112 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.6974 (tm-30) REVERT: D 134 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7749 (mt) REVERT: D 406 SER cc_start: 0.8109 (t) cc_final: 0.7665 (p) REVERT: E 389 GLU cc_start: 0.6876 (tt0) cc_final: 0.6411 (tp30) REVERT: E 392 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6701 (mm-30) REVERT: E 414 TRP cc_start: 0.7294 (m-90) cc_final: 0.6597 (m-90) REVERT: F 1 MET cc_start: 0.7910 (ptt) cc_final: 0.7465 (ptt) REVERT: F 181 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7150 (ttmm) REVERT: F 243 ASP cc_start: 0.7231 (m-30) cc_final: 0.6902 (t0) REVERT: F 321 ILE cc_start: 0.7311 (mt) cc_final: 0.6666 (mt) REVERT: F 326 GLU cc_start: 0.6047 (OUTLIER) cc_final: 0.5604 (mp0) REVERT: F 399 GLN cc_start: 0.6741 (OUTLIER) cc_final: 0.6497 (tp40) REVERT: H 130 LEU cc_start: 0.2406 (OUTLIER) cc_final: 0.2048 (tp) REVERT: H 158 GLU cc_start: 0.3120 (OUTLIER) cc_final: 0.2720 (pm20) REVERT: H 244 ASN cc_start: 0.6713 (m-40) cc_final: 0.6352 (t0) REVERT: H 278 ILE cc_start: 0.8344 (pp) cc_final: 0.8144 (mm) REVERT: H 281 MET cc_start: 0.7630 (mmt) cc_final: 0.7204 (mmm) REVERT: H 295 ASP cc_start: 0.6499 (p0) cc_final: 0.6185 (p0) outliers start: 99 outliers final: 60 residues processed: 412 average time/residue: 0.1516 time to fit residues: 97.7768 Evaluate side-chains 371 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 301 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 175 LYS Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain H residue 331 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 64 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 252 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 181 optimal weight: 0.9990 chunk 229 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 157 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 235 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 200 ASN C 125 ASN D 114 GLN D 288 ASN ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.145567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.120270 restraints weight = 39616.326| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.15 r_work: 0.3375 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24197 Z= 0.156 Angle : 0.576 8.190 32807 Z= 0.308 Chirality : 0.044 0.224 3647 Planarity : 0.004 0.047 4071 Dihedral : 10.618 164.147 3352 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.41 % Allowed : 15.10 % Favored : 81.49 % 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: -0.09 (0.16), residues: 2898 helix: 1.10 (0.14), residues: 1450 sheet: -0.53 (0.27), residues: 396 loop : -1.48 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 320 TYR 0.030 0.001 TYR H 86 PHE 0.016 0.002 PHE H 81 TRP 0.019 0.001 TRP H 150 HIS 0.006 0.001 HIS H 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (24197) covalent geometry : angle 0.57590 / 0.31 (32807) hydrogen bonds : bond 0.03778 / 2.57 ( 1158) hydrogen bonds : angle 4.91431 / 3.53 ( 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 405 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 319 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7542 (mttm) cc_final: 0.7164 (ttmm) REVERT: A 74 LYS cc_start: 0.6876 (tptp) cc_final: 0.6354 (ttpp) REVERT: A 291 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.6854 (ttm-80) REVERT: A 345 GLU cc_start: 0.7951 (tp30) cc_final: 0.7730 (tp30) REVERT: C 74 LYS cc_start: 0.6885 (mmtt) cc_final: 0.6590 (mmmm) REVERT: C 175 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7915 (tttm) REVERT: C 431 ILE cc_start: 0.7043 (mm) cc_final: 0.6828 (mt) REVERT: D 406 SER cc_start: 0.8119 (t) cc_final: 0.7685 (p) REVERT: E 389 GLU cc_start: 0.6848 (tt0) cc_final: 0.6427 (tp30) REVERT: E 392 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6737 (mm-30) REVERT: E 414 TRP cc_start: 0.7339 (m-90) cc_final: 0.6628 (m-90) REVERT: F 181 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7047 (ttmm) REVERT: F 243 ASP cc_start: 0.7197 (m-30) cc_final: 0.6897 (t0) REVERT: F 321 ILE cc_start: 0.7221 (mt) cc_final: 0.6659 (mt) REVERT: F 326 GLU cc_start: 0.6018 (OUTLIER) cc_final: 0.5684 (mp0) REVERT: F 399 GLN cc_start: 0.6939 (OUTLIER) cc_final: 0.6637 (tp40) REVERT: F 418 LEU cc_start: 0.6023 (OUTLIER) cc_final: 0.5615 (tp) REVERT: H 80 GLU cc_start: 0.7887 (mm-30) cc_final: 0.6616 (mp0) REVERT: H 130 LEU cc_start: 0.2557 (OUTLIER) cc_final: 0.2270 (tp) REVERT: H 158 GLU cc_start: 0.3175 (OUTLIER) cc_final: 0.2785 (pm20) REVERT: H 244 ASN cc_start: 0.6731 (m-40) cc_final: 0.6345 (t0) REVERT: H 281 MET cc_start: 0.7646 (mmt) cc_final: 0.7227 (mmm) REVERT: H 295 ASP cc_start: 0.6401 (p0) cc_final: 0.5814 (p0) outliers start: 86 outliers final: 64 residues processed: 381 average time/residue: 0.1538 time to fit residues: 91.8077 Evaluate side-chains 370 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 298 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 175 LYS Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain H residue 331 MET 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: 0.9980 chunk 28 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 270 optimal weight: 0.4980 chunk 246 optimal weight: 10.0000 chunk 286 optimal weight: 0.6980 chunk 256 optimal weight: 0.6980 chunk 269 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 200 ASN D 114 GLN D 288 ASN ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN F 200 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.147309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.122323 restraints weight = 39055.750| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.11 r_work: 0.3408 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 24197 Z= 0.114 Angle : 0.537 9.585 32807 Z= 0.287 Chirality : 0.042 0.210 3647 Planarity : 0.003 0.046 4071 Dihedral : 10.453 164.444 3352 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.66 % Allowed : 15.93 % Favored : 81.41 % 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: 0.14 (0.16), residues: 2898 helix: 1.32 (0.14), residues: 1456 sheet: -0.42 (0.27), residues: 403 loop : -1.45 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 124 TYR 0.029 0.001 TYR H 86 PHE 0.012 0.001 PHE A 417 TRP 0.018 0.001 TRP H 266 HIS 0.007 0.001 HIS H 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (24197) covalent geometry : angle 0.53655 / 0.29 (32807) hydrogen bonds : bond 0.03384 / 2.32 ( 1158) hydrogen bonds : angle 4.75143 / 3.41 ( 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 393 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 326 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7839 (mp0) cc_final: 0.7533 (mp0) REVERT: A 38 LYS cc_start: 0.7477 (mttm) cc_final: 0.7131 (ttmm) REVERT: B 312 TYR cc_start: 0.4693 (t80) cc_final: 0.4428 (t80) REVERT: C 13 GLN cc_start: 0.7301 (tp-100) cc_final: 0.6963 (mm-40) REVERT: C 69 GLU cc_start: 0.6794 (mm-30) cc_final: 0.6524 (mm-30) REVERT: C 431 ILE cc_start: 0.7017 (mm) cc_final: 0.6807 (mt) REVERT: D 134 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7761 (mt) REVERT: D 406 SER cc_start: 0.8050 (t) cc_final: 0.7642 (p) REVERT: E 392 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6591 (mm-30) REVERT: E 414 TRP cc_start: 0.7314 (m-90) cc_final: 0.6039 (m-90) REVERT: F 181 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7012 (ttmm) REVERT: F 321 ILE cc_start: 0.7144 (mt) cc_final: 0.6234 (mt) REVERT: F 326 GLU cc_start: 0.5976 (OUTLIER) cc_final: 0.5543 (mp0) REVERT: F 399 GLN cc_start: 0.6846 (OUTLIER) cc_final: 0.6544 (tp40) REVERT: F 418 LEU cc_start: 0.6185 (OUTLIER) cc_final: 0.5737 (tp) REVERT: H 80 GLU cc_start: 0.7796 (mm-30) cc_final: 0.6614 (mp0) REVERT: H 130 LEU cc_start: 0.2422 (OUTLIER) cc_final: 0.2108 (tp) REVERT: H 158 GLU cc_start: 0.3289 (OUTLIER) cc_final: 0.2874 (pm20) REVERT: H 244 ASN cc_start: 0.6798 (m-40) cc_final: 0.6375 (t0) REVERT: H 281 MET cc_start: 0.7590 (mmt) cc_final: 0.7117 (mmm) REVERT: H 282 THR cc_start: 0.8009 (m) cc_final: 0.7700 (p) REVERT: H 295 ASP cc_start: 0.6390 (p0) cc_final: 0.5762 (p0) outliers start: 67 outliers final: 49 residues processed: 373 average time/residue: 0.1472 time to fit residues: 87.0071 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 : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 175 LYS Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 200 ASN Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain H residue 331 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 203 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 252 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 247 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 ASN ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN H 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.147670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.122529 restraints weight = 39126.209| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.05 r_work: 0.3410 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24197 Z= 0.118 Angle : 0.538 11.012 32807 Z= 0.287 Chirality : 0.042 0.212 3647 Planarity : 0.003 0.043 4071 Dihedral : 10.420 164.782 3352 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.70 % Allowed : 16.29 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.16), residues: 2898 helix: 1.40 (0.14), residues: 1457 sheet: -0.33 (0.27), residues: 401 loop : -1.44 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 340 TYR 0.025 0.001 TYR H 86 PHE 0.012 0.001 PHE H 81 TRP 0.012 0.001 TRP C 20 HIS 0.007 0.001 HIS H 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (24197) covalent geometry : angle 0.53810 / 0.29 (32807) hydrogen bonds : bond 0.03315 / 2.26 ( 1158) hydrogen bonds : angle 4.67661 / 3.36 ( 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 378 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 310 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7489 (mttm) cc_final: 0.7140 (ttmm) REVERT: A 74 LYS cc_start: 0.6784 (tptp) cc_final: 0.6252 (ttpp) REVERT: B 391 GLU cc_start: 0.7340 (tp30) cc_final: 0.7026 (tp30) REVERT: C 13 GLN cc_start: 0.7349 (tp-100) cc_final: 0.7008 (mm-40) REVERT: C 69 GLU cc_start: 0.6684 (mm-30) cc_final: 0.6452 (mm-30) REVERT: C 175 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7920 (tttm) REVERT: D 95 GLU cc_start: 0.8318 (tp30) cc_final: 0.8077 (mm-30) REVERT: D 134 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7810 (mt) REVERT: D 373 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7037 (tp30) REVERT: D 406 SER cc_start: 0.8043 (t) cc_final: 0.7618 (p) REVERT: E 392 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6591 (mm-30) REVERT: E 414 TRP cc_start: 0.7318 (m-90) cc_final: 0.6659 (m-90) REVERT: F 181 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7007 (ttmm) REVERT: F 241 MET cc_start: 0.7765 (mmm) cc_final: 0.7220 (mmp) REVERT: F 321 ILE cc_start: 0.7122 (mt) cc_final: 0.6232 (mt) REVERT: F 326 GLU cc_start: 0.5993 (OUTLIER) cc_final: 0.5544 (mp0) REVERT: F 399 GLN cc_start: 0.6887 (OUTLIER) cc_final: 0.6603 (tp40) REVERT: F 418 LEU cc_start: 0.6244 (OUTLIER) cc_final: 0.5812 (tp) REVERT: H 80 GLU cc_start: 0.7756 (mm-30) cc_final: 0.6566 (mp0) REVERT: H 130 LEU cc_start: 0.2340 (OUTLIER) cc_final: 0.1999 (tp) REVERT: H 158 GLU cc_start: 0.3297 (OUTLIER) cc_final: 0.2942 (pm20) REVERT: H 244 ASN cc_start: 0.6796 (m-40) cc_final: 0.6088 (t0) REVERT: H 281 MET cc_start: 0.7592 (mmt) cc_final: 0.7120 (mmm) REVERT: H 282 THR cc_start: 0.8028 (m) cc_final: 0.7708 (p) REVERT: H 295 ASP cc_start: 0.6381 (p0) cc_final: 0.5749 (p0) outliers start: 68 outliers final: 54 residues processed: 362 average time/residue: 0.1417 time to fit residues: 80.9284 Evaluate side-chains 357 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 295 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 175 LYS Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 260 LYS Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 170 ARG Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 308 ILE 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: 5.9990 chunk 83 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 74 optimal weight: 0.0370 chunk 276 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 179 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN C 398 GLN ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN H 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.144892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.119908 restraints weight = 39578.603| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.16 r_work: 0.3371 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24197 Z= 0.191 Angle : 0.602 11.788 32807 Z= 0.319 Chirality : 0.044 0.229 3647 Planarity : 0.004 0.051 4071 Dihedral : 10.623 166.226 3351 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.01 % Allowed : 15.97 % Favored : 81.01 % 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: 0.02 (0.16), residues: 2898 helix: 1.21 (0.14), residues: 1454 sheet: -0.47 (0.26), residues: 400 loop : -1.48 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 94 TYR 0.024 0.002 TYR H 86 PHE 0.019 0.002 PHE D 37 TRP 0.016 0.002 TRP A 162 HIS 0.007 0.001 HIS H 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (24197) covalent geometry : angle 0.60179 / 0.32 (32807) hydrogen bonds : bond 0.03754 / 2.55 ( 1158) hydrogen bonds : angle 4.81667 / 3.46 ( 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 390 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 314 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7957 (mp0) cc_final: 0.7482 (mp0) REVERT: A 38 LYS cc_start: 0.7539 (mttm) cc_final: 0.7197 (ttmm) REVERT: A 69 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6299 (mp0) REVERT: A 74 LYS cc_start: 0.6865 (tptp) cc_final: 0.6354 (ttpp) REVERT: A 291 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.6962 (ttm-80) REVERT: B 391 GLU cc_start: 0.7285 (tp30) cc_final: 0.6967 (tp30) REVERT: C 47 TYR cc_start: 0.5686 (OUTLIER) cc_final: 0.5057 (m-10) REVERT: C 124 ARG cc_start: 0.6808 (ptp-110) cc_final: 0.5848 (mtm-85) REVERT: C 142 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7353 (mt) REVERT: C 175 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7919 (tttm) REVERT: D 95 GLU cc_start: 0.8327 (tp30) cc_final: 0.8102 (mm-30) REVERT: D 134 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7832 (mt) REVERT: D 373 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7194 (tp30) REVERT: E 389 GLU cc_start: 0.6850 (tt0) cc_final: 0.6496 (tp30) REVERT: E 392 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6751 (mm-30) REVERT: E 414 TRP cc_start: 0.7362 (m-90) cc_final: 0.6777 (m-90) REVERT: F 181 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7200 (ttmm) REVERT: F 243 ASP cc_start: 0.7173 (m-30) cc_final: 0.6889 (t0) REVERT: F 321 ILE cc_start: 0.7215 (mt) cc_final: 0.6624 (mt) REVERT: F 326 GLU cc_start: 0.6016 (OUTLIER) cc_final: 0.5608 (mp0) REVERT: F 399 GLN cc_start: 0.7010 (OUTLIER) cc_final: 0.6708 (tp40) REVERT: F 418 LEU cc_start: 0.6298 (OUTLIER) cc_final: 0.5803 (tp) REVERT: H 80 GLU cc_start: 0.7820 (mm-30) cc_final: 0.6653 (mp0) REVERT: H 130 LEU cc_start: 0.2495 (OUTLIER) cc_final: 0.2160 (tp) REVERT: H 158 GLU cc_start: 0.3310 (OUTLIER) cc_final: 0.2799 (pm20) REVERT: H 194 PHE cc_start: 0.3553 (p90) cc_final: 0.3107 (p90) REVERT: H 244 ASN cc_start: 0.6804 (m-40) cc_final: 0.6174 (t0) REVERT: H 281 MET cc_start: 0.7644 (mmt) cc_final: 0.7235 (mmm) REVERT: H 295 ASP cc_start: 0.6376 (p0) cc_final: 0.6085 (p0) outliers start: 76 outliers final: 59 residues processed: 372 average time/residue: 0.1470 time to fit residues: 85.9922 Evaluate side-chains 369 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 298 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 175 LYS Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 260 LYS Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain H residue 331 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 242 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 83 optimal weight: 0.0040 chunk 179 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 208 optimal weight: 4.9990 chunk 241 optimal weight: 5.9990 chunk 135 optimal weight: 0.1980 chunk 184 optimal weight: 0.0060 overall best weight: 0.8410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 399 GLN ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 HIS H 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.147453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.122573 restraints weight = 39432.176| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.17 r_work: 0.3404 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 24197 Z= 0.113 Angle : 0.550 11.579 32807 Z= 0.293 Chirality : 0.042 0.220 3647 Planarity : 0.003 0.039 4071 Dihedral : 10.441 166.716 3351 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.18 % Allowed : 17.08 % Favored : 80.74 % 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: 1.38 (0.14), residues: 1462 sheet: -0.36 (0.27), residues: 395 loop : -1.42 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 94 TYR 0.022 0.001 TYR H 220 PHE 0.012 0.001 PHE B 417 TRP 0.019 0.001 TRP H 159 HIS 0.007 0.001 HIS H 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (24197) covalent geometry : angle 0.55028 / 0.29 (32807) hydrogen bonds : bond 0.03275 / 2.24 ( 1158) hydrogen bonds : angle 4.68201 / 3.36 ( 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 362 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 307 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7908 (mp0) cc_final: 0.7456 (mp0) REVERT: A 38 LYS cc_start: 0.7396 (mttm) cc_final: 0.7024 (ttmm) REVERT: A 74 LYS cc_start: 0.6827 (tptp) cc_final: 0.6286 (ttpp) REVERT: A 243 ASP cc_start: 0.7999 (m-30) cc_final: 0.7571 (m-30) REVERT: B 391 GLU cc_start: 0.7285 (tp30) cc_final: 0.6977 (tp30) REVERT: C 13 GLN cc_start: 0.7405 (tp-100) cc_final: 0.7055 (mm-40) REVERT: C 175 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7892 (tttm) REVERT: D 95 GLU cc_start: 0.8139 (tp30) cc_final: 0.7920 (mm-30) REVERT: D 134 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7818 (mt) REVERT: D 406 SER cc_start: 0.8094 (t) cc_final: 0.7681 (p) REVERT: E 392 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6640 (mm-30) REVERT: E 414 TRP cc_start: 0.7364 (m-90) cc_final: 0.6322 (m-90) REVERT: F 181 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7044 (ttmm) REVERT: F 247 ASP cc_start: 0.6533 (m-30) cc_final: 0.6295 (m-30) REVERT: F 321 ILE cc_start: 0.7172 (mt) cc_final: 0.6920 (mt) REVERT: F 326 GLU cc_start: 0.6030 (OUTLIER) cc_final: 0.5665 (mp0) REVERT: F 399 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.6658 (tp40) REVERT: H 80 GLU cc_start: 0.7682 (mm-30) cc_final: 0.6507 (mp0) REVERT: H 130 LEU cc_start: 0.2555 (OUTLIER) cc_final: 0.2220 (tp) REVERT: H 158 GLU cc_start: 0.3433 (OUTLIER) cc_final: 0.3147 (pm20) REVERT: H 244 ASN cc_start: 0.6779 (m-40) cc_final: 0.6327 (t0) REVERT: H 281 MET cc_start: 0.7583 (mmt) cc_final: 0.7184 (mmm) REVERT: H 295 ASP cc_start: 0.6346 (p0) cc_final: 0.5726 (p0) outliers start: 55 outliers final: 43 residues processed: 349 average time/residue: 0.1527 time to fit residues: 83.8441 Evaluate side-chains 336 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 286 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 175 LYS Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 260 LYS Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 8 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 170 ARG Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 331 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 52 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 273 optimal weight: 8.9990 chunk 226 optimal weight: 10.0000 chunk 251 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 200 ASN B 399 GLN ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.146685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.122055 restraints weight = 39384.585| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.09 r_work: 0.3400 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24197 Z= 0.148 Angle : 0.567 11.056 32807 Z= 0.301 Chirality : 0.043 0.228 3647 Planarity : 0.003 0.040 4071 Dihedral : 10.490 167.435 3351 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.14 % Allowed : 17.56 % Favored : 80.30 % 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: 0.19 (0.16), residues: 2898 helix: 1.36 (0.14), residues: 1462 sheet: -0.43 (0.27), residues: 400 loop : -1.42 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 94 TYR 0.021 0.001 TYR H 86 PHE 0.020 0.002 PHE H 194 TRP 0.022 0.001 TRP H 159 HIS 0.015 0.001 HIS F 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (24197) covalent geometry : angle 0.56657 / 0.30 (32807) hydrogen bonds : bond 0.03455 / 2.35 ( 1158) hydrogen bonds : angle 4.68835 / 3.36 ( 3303) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4745.95 seconds wall clock time: 82 minutes 40.16 seconds (4960.16 seconds total)