Starting phenix.real_space_refine on Sun Sep 13 13:11:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dvf_27737/09_2026/8dvf_27737.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dvf_27737/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8dvf_27737/09_2026/8dvf_27737.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dvf_27737/09_2026/8dvf_27737.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dvf_27737/09_2026/8dvf_27737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dvf_27737/09_2026/8dvf_27737.map" model { file = "/net/cci-nas-00/data/ceres_data/8dvf_27737/09_2026/8dvf_27737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dvf_27737/09_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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23693 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "B" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "C" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "D" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "E" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "F" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "M" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "H" Number of atoms: 2644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2644 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain breaks: 1 Chain: "T" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.85, per 1000 atoms: 0.20 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: 1.80 Conformation dependent library (CDL) restraints added in 833.1 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: 0.70 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: 3.43 Time building geometry restraints manager: 2.47 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: 2.050 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: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.940 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.300 ------------------------------------------------------------------------------- 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 0.68912 / 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 : 0.756 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: 0.7430 (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: 0.5938 (mtp) REVERT: A 292 SER cc_start: 0.7262 (p) cc_final: 0.7025 (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: 0.6526 (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: 0.6697 (p0) REVERT: F 399 GLN cc_start: 0.6490 (OUTLIER) cc_final: 0.5585 (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: 0.5417 (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: 0.3857 (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: 0.3724 (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: 0.6484 (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: 0.5794 (m-80) REVERT: H 322 MET cc_start: 0.6755 (mtm) cc_final: 0.6541 (mtm) outliers start: 45 outliers final: 7 residues processed: 794 average time/residue: 0.1774 time to fit residues: 211.8494 Evaluate side-chains 395 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 385 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 D 403 GLN E 57 ASN E 114 GLN F 398 GLN H 195 GLN H 328 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.151579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.126899 restraints weight = 39599.506| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.13 r_work: 0.3477 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 24197 Z= 0.160 Angle : 0.602 6.569 32807 Z= 0.327 Chirality : 0.044 0.201 3647 Planarity : 0.004 0.069 4071 Dihedral : 10.352 171.724 3363 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.58 % Allowed : 12.17 % Favored : 85.26 % 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 (0.16), residues: 2898 helix: 1.30 (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 0.010 0.001 ARG C 124 TYR 0.023 0.002 TYR H 13 PHE 0.013 0.002 PHE C 37 TRP 0.023 0.001 TRP H 266 HIS 0.009 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (24197) covalent geometry : angle 0.60172 / 0.33 (32807) hydrogen bonds : bond 0.04409 / 2.99 ( 1158) hydrogen bonds : angle 5.24507 / 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 470 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 405 time to evaluate : 0.979 Fit side-chains REVERT: A 19 VAL cc_start: 0.8420 (OUTLIER) cc_final: 0.8206 (t) REVERT: A 22 TYR cc_start: 0.7958 (m-80) cc_final: 0.7441 (m-80) REVERT: A 419 MET cc_start: 0.7445 (tpp) cc_final: 0.6901 (tpt) REVERT: C 85 GLU cc_start: 0.6753 (mm-30) cc_final: 0.6466 (mm-30) REVERT: C 157 ASP cc_start: 0.7770 (m-30) cc_final: 0.7478 (m-30) REVERT: D 103 MET cc_start: 0.7190 (mmm) cc_final: 0.6961 (mtp) REVERT: D 264 GLU cc_start: 0.6669 (mm-30) cc_final: 0.6454 (mm-30) REVERT: E 228 MET cc_start: 0.7640 (mtm) cc_final: 0.7264 (ptm) REVERT: E 392 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6257 (mm-30) REVERT: E 413 LYS cc_start: 0.7090 (tppt) cc_final: 0.6801 (tppp) REVERT: E 414 TRP cc_start: 0.7251 (m-90) cc_final: 0.6657 (m-90) REVERT: F 311 ASP cc_start: 0.7422 (t0) cc_final: 0.6784 (p0) REVERT: F 418 LEU cc_start: 0.6038 (OUTLIER) cc_final: 0.5736 (tt) REVERT: H 80 GLU cc_start: 0.7689 (mm-30) cc_final: 0.5944 (pt0) REVERT: H 244 ASN cc_start: 0.6551 (m-40) cc_final: 0.6329 (t0) REVERT: H 264 ARG cc_start: 0.6779 (ptt180) cc_final: 0.6100 (ptt180) REVERT: H 278 ILE cc_start: 0.8398 (pp) cc_final: 0.7879 (mm) REVERT: H 281 MET cc_start: 0.7649 (mmt) cc_final: 0.7121 (mmm) outliers start: 65 outliers final: 33 residues processed: 450 average time/residue: 0.1557 time to fit residues: 110.6826 Evaluate side-chains 352 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 317 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 201 VAL 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 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: 0.9980 chunk 150 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 178 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 chunk 244 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN B 200 ASN B 355 GLN C 35 ASN C 125 ASN D 114 GLN D 167 ASN D 399 GLN D 403 GLN F 57 ASN H 325 ASN H 328 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.149525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.124394 restraints weight = 39415.614| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.04 r_work: 0.3443 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24197 Z= 0.155 Angle : 0.577 8.004 32807 Z= 0.311 Chirality : 0.043 0.236 3647 Planarity : 0.004 0.082 4071 Dihedral : 10.369 168.338 3356 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.89 % Allowed : 13.63 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.16), residues: 2898 helix: 1.27 (0.14), residues: 1450 sheet: -0.25 (0.27), residues: 395 loop : -1.26 (0.18), residues: 1053 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 0.021 0.001 TRP A 361 HIS 0.005 0.001 HIS H 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (24197) covalent geometry : angle 0.57683 / 0.31 (32807) hydrogen bonds : bond 0.03954 / 2.69 ( 1158) hydrogen bonds : angle 4.95331 / 3.55 ( 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 433 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 360 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: A 19 VAL cc_start: 0.8425 (OUTLIER) cc_final: 0.8173 (t) REVERT: A 38 LYS cc_start: 0.7572 (mttm) cc_final: 0.6853 (mmtm) REVERT: C 85 GLU cc_start: 0.6958 (mm-30) cc_final: 0.6695 (mm-30) REVERT: C 157 ASP cc_start: 0.7868 (m-30) cc_final: 0.7613 (m-30) REVERT: D 103 MET cc_start: 0.7249 (mmm) cc_final: 0.7000 (mtp) REVERT: D 264 GLU cc_start: 0.6496 (mm-30) cc_final: 0.6200 (mm-30) REVERT: E 392 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6423 (mm-30) REVERT: E 414 TRP cc_start: 0.7300 (m-90) cc_final: 0.6651 (m-90) REVERT: F 311 ASP cc_start: 0.7552 (t0) cc_final: 0.6609 (p0) REVERT: F 321 ILE cc_start: 0.7188 (mt) cc_final: 0.6287 (mt) REVERT: F 399 GLN cc_start: 0.6761 (OUTLIER) cc_final: 0.6324 (tp40) REVERT: F 418 LEU cc_start: 0.6020 (OUTLIER) cc_final: 0.5613 (tt) REVERT: H 80 GLU cc_start: 0.7777 (mm-30) cc_final: 0.6417 (tt0) REVERT: H 213 TYR cc_start: 0.4539 (p90) cc_final: 0.4176 (p90) REVERT: H 244 ASN cc_start: 0.6648 (m-40) cc_final: 0.6386 (t0) REVERT: H 278 ILE cc_start: 0.8295 (pp) cc_final: 0.7982 (mm) REVERT: H 281 MET cc_start: 0.7753 (mmt) cc_final: 0.7176 (mmm) REVERT: H 292 MET cc_start: 0.7728 (tpt) cc_final: 0.7493 (tpt) outliers start: 73 outliers final: 46 residues processed: 410 average time/residue: 0.1577 time to fit residues: 101.2325 Evaluate side-chains 359 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 310 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 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 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 25 SER Chi-restraints excluded: chain C residue 196 MET 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 25 SER 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 254 ILE 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 194 optimal weight: 10.0000 chunk 236 optimal weight: 8.9990 chunk 191 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 chunk 268 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 289 optimal weight: 10.0000 chunk 288 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 285 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 114 GLN D 167 ASN E 200 ASN F 216 GLN H 188 ASN H 195 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.149878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.124713 restraints weight = 39360.168| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.11 r_work: 0.3442 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24197 Z= 0.123 Angle : 0.531 7.194 32807 Z= 0.288 Chirality : 0.042 0.242 3647 Planarity : 0.003 0.043 4071 Dihedral : 10.345 171.180 3354 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.73 % Allowed : 14.47 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.16), residues: 2898 helix: 1.36 (0.14), residues: 1449 sheet: -0.28 (0.27), residues: 397 loop : -1.27 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 320 TYR 0.015 0.001 TYR H 185 PHE 0.012 0.002 PHE C 37 TRP 0.010 0.001 TRP F 89 HIS 0.005 0.001 HIS H 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (24197) covalent geometry : angle 0.53104 / 0.29 (32807) hydrogen bonds : bond 0.03529 / 2.39 ( 1158) hydrogen bonds : angle 4.83047 / 3.46 ( 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 408 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 339 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7541 (mttm) cc_final: 0.7048 (ttmm) REVERT: B 1 MET cc_start: 0.7899 (ptp) cc_final: 0.7699 (ptm) REVERT: C 85 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6781 (mm-30) REVERT: C 157 ASP cc_start: 0.7878 (m-30) cc_final: 0.7604 (m-30) REVERT: D 103 MET cc_start: 0.7256 (mmm) cc_final: 0.7022 (mtp) REVERT: D 134 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7835 (mt) REVERT: E 259 TYR cc_start: 0.7829 (t80) cc_final: 0.7440 (t80) REVERT: E 392 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6485 (mm-30) REVERT: E 414 TRP cc_start: 0.7292 (m-90) cc_final: 0.6193 (m-90) REVERT: F 1 MET cc_start: 0.7348 (ptt) cc_final: 0.7057 (ptt) REVERT: F 181 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.6907 (ttmm) REVERT: F 326 GLU cc_start: 0.5947 (mp0) cc_final: 0.5497 (mp0) REVERT: F 399 GLN cc_start: 0.6719 (OUTLIER) cc_final: 0.6257 (tp40) REVERT: F 418 LEU cc_start: 0.6075 (OUTLIER) cc_final: 0.5645 (tt) REVERT: H 80 GLU cc_start: 0.7786 (mm-30) cc_final: 0.6577 (tm-30) REVERT: H 213 TYR cc_start: 0.4394 (p90) cc_final: 0.4047 (p90) REVERT: H 244 ASN cc_start: 0.6782 (m-40) cc_final: 0.6430 (t0) REVERT: H 264 ARG cc_start: 0.6660 (ptt180) cc_final: 0.6455 (ptt180) REVERT: H 278 ILE cc_start: 0.8292 (pp) cc_final: 0.8039 (mm) REVERT: H 281 MET cc_start: 0.7673 (mmt) cc_final: 0.7131 (mmm) REVERT: H 282 THR cc_start: 0.7923 (m) cc_final: 0.7534 (p) REVERT: H 292 MET cc_start: 0.7844 (tpt) cc_final: 0.7530 (tpt) outliers start: 69 outliers final: 49 residues processed: 390 average time/residue: 0.1574 time to fit residues: 97.5889 Evaluate side-chains 365 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 312 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR 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 17 SER 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 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 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 200 ASN 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 8 HIS 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 227 GLU Chi-restraints excluded: chain F residue 282 THR 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 F residue 431 ILE 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 331 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 3 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 283 optimal weight: 20.0000 chunk 253 optimal weight: 6.9990 chunk 282 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 266 optimal weight: 1.9990 chunk 281 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 226 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 200 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN D 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.146904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.121634 restraints weight = 39342.933| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.10 r_work: 0.3394 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24197 Z= 0.187 Angle : 0.585 8.931 32807 Z= 0.315 Chirality : 0.044 0.242 3647 Planarity : 0.004 0.049 4071 Dihedral : 10.524 166.299 3354 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.65 % Allowed : 14.03 % Favored : 82.32 % 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: 0.10 (0.16), residues: 2898 helix: 1.24 (0.14), residues: 1448 sheet: -0.48 (0.26), residues: 405 loop : -1.34 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 126 TYR 0.030 0.002 TYR H 86 PHE 0.017 0.002 PHE D 37 TRP 0.013 0.002 TRP A 162 HIS 0.006 0.001 HIS H 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (24197) covalent geometry : angle 0.58548 / 0.31 (32807) hydrogen bonds : bond 0.03812 / 2.57 ( 1158) hydrogen bonds : angle 4.87325 / 3.50 ( 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 417 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 325 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7540 (mttm) cc_final: 0.7087 (ttmm) REVERT: A 345 GLU cc_start: 0.8032 (tp30) cc_final: 0.7755 (tp30) REVERT: C 175 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7945 (tttm) REVERT: D 134 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7690 (mt) REVERT: D 175 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7804 (mtpt) REVERT: D 406 SER cc_start: 0.7874 (t) cc_final: 0.7599 (p) REVERT: E 389 GLU cc_start: 0.6793 (tt0) cc_final: 0.6331 (tp30) REVERT: E 392 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6434 (mm-30) REVERT: E 414 TRP cc_start: 0.7356 (m-90) cc_final: 0.6201 (m-90) REVERT: F 181 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7037 (ttmm) REVERT: F 326 GLU cc_start: 0.5996 (mt-10) cc_final: 0.5569 (mp0) REVERT: F 399 GLN cc_start: 0.6778 (OUTLIER) cc_final: 0.6519 (tp40) REVERT: H 80 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7167 (mp0) REVERT: H 158 GLU cc_start: 0.3150 (OUTLIER) cc_final: 0.2879 (pm20) REVERT: H 244 ASN cc_start: 0.6768 (m-40) cc_final: 0.6392 (t0) REVERT: H 278 ILE cc_start: 0.8329 (pp) cc_final: 0.8116 (mm) REVERT: H 281 MET cc_start: 0.7612 (mmt) cc_final: 0.7157 (mmm) REVERT: H 295 ASP cc_start: 0.6420 (p0) cc_final: 0.5748 (p0) outliers start: 92 outliers final: 55 residues processed: 392 average time/residue: 0.1587 time to fit residues: 97.6637 Evaluate side-chains 356 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 295 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 425 ASN 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 201 VAL 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 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 319 CYS Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 421 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 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 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 399 GLN Chi-restraints excluded: chain H residue 88 GLU 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: 4.9990 chunk 192 optimal weight: 3.9990 chunk 252 optimal weight: 0.3980 chunk 55 optimal weight: 8.9990 chunk 181 optimal weight: 0.9990 chunk 229 optimal weight: 9.9990 chunk 36 optimal weight: 0.0970 chunk 157 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 235 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 ASN B 200 ASN C 114 GLN D 114 GLN D 167 ASN E 403 GLN F 398 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.148152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.123063 restraints weight = 39359.340| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.07 r_work: 0.3425 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24197 Z= 0.120 Angle : 0.530 8.303 32807 Z= 0.286 Chirality : 0.042 0.233 3647 Planarity : 0.003 0.038 4071 Dihedral : 10.393 170.310 3351 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.85 % Allowed : 14.82 % Favored : 82.32 % 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 (0.16), residues: 2898 helix: 1.41 (0.14), residues: 1445 sheet: -0.37 (0.27), residues: 403 loop : -1.32 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 94 TYR 0.032 0.001 TYR H 86 PHE 0.014 0.002 PHE A 417 TRP 0.011 0.001 TRP B 162 HIS 0.008 0.001 HIS D 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (24197) covalent geometry : angle 0.52981 / 0.29 (32807) hydrogen bonds : bond 0.03435 / 2.33 ( 1158) hydrogen bonds : angle 4.76024 / 3.42 ( 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 399 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 327 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7882 (mp0) cc_final: 0.7442 (mp0) REVERT: A 38 LYS cc_start: 0.7461 (mttm) cc_final: 0.7046 (ttmm) REVERT: A 345 GLU cc_start: 0.7877 (tp30) cc_final: 0.7662 (tp30) REVERT: B 1 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7615 (ptp) REVERT: C 118 GLU cc_start: 0.6373 (tm-30) cc_final: 0.5469 (tt0) REVERT: D 134 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7684 (mt) REVERT: D 406 SER cc_start: 0.7914 (t) cc_final: 0.7551 (p) REVERT: E 228 MET cc_start: 0.7725 (ptp) cc_final: 0.7290 (ptm) REVERT: E 389 GLU cc_start: 0.6728 (tt0) cc_final: 0.6340 (tp30) REVERT: E 392 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6473 (mm-30) REVERT: E 413 LYS cc_start: 0.7287 (tppt) cc_final: 0.6751 (tptp) REVERT: E 414 TRP cc_start: 0.7302 (m-90) cc_final: 0.6150 (m-90) REVERT: F 181 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.6948 (ttmm) REVERT: F 326 GLU cc_start: 0.5961 (mt-10) cc_final: 0.5621 (mp0) REVERT: F 399 GLN cc_start: 0.6904 (OUTLIER) cc_final: 0.6610 (tp40) REVERT: H 80 GLU cc_start: 0.7823 (mm-30) cc_final: 0.6498 (mp0) REVERT: H 94 ARG cc_start: 0.7671 (mmm-85) cc_final: 0.7127 (mmm160) REVERT: H 158 GLU cc_start: 0.3193 (OUTLIER) cc_final: 0.2968 (pm20) REVERT: H 244 ASN cc_start: 0.6783 (m-40) cc_final: 0.6398 (t0) REVERT: H 281 MET cc_start: 0.7578 (mmt) cc_final: 0.7124 (mmm) REVERT: H 295 ASP cc_start: 0.6377 (p0) cc_final: 0.5764 (p0) outliers start: 72 outliers final: 49 residues processed: 379 average time/residue: 0.1557 time to fit residues: 93.7330 Evaluate side-chains 349 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 295 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 425 ASN Chi-restraints excluded: chain B residue 1 MET 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 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 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 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 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 E residue 344 VAL Chi-restraints excluded: chain F residue 2 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 178 ILE Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain F residue 399 GLN 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 233 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 270 optimal weight: 7.9990 chunk 246 optimal weight: 10.0000 chunk 286 optimal weight: 6.9990 chunk 256 optimal weight: 5.9990 chunk 269 optimal weight: 0.4980 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN C 125 ASN D 114 GLN D 167 ASN ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.145834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.121146 restraints weight = 39280.089| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.99 r_work: 0.3399 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24197 Z= 0.189 Angle : 0.601 13.427 32807 Z= 0.319 Chirality : 0.044 0.244 3647 Planarity : 0.004 0.044 4071 Dihedral : 10.598 166.417 3351 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.37 % Allowed : 14.94 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.16), residues: 2898 helix: 1.22 (0.14), residues: 1449 sheet: -0.49 (0.27), residues: 401 loop : -1.43 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 126 TYR 0.031 0.002 TYR H 86 PHE 0.019 0.002 PHE D 37 TRP 0.022 0.002 TRP H 266 HIS 0.012 0.001 HIS H 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (24197) covalent geometry : angle 0.60064 / 0.32 (32807) hydrogen bonds : bond 0.03795 / 2.56 ( 1158) hydrogen bonds : angle 4.86391 / 3.49 ( 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 402 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 317 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8115 (mp0) cc_final: 0.7744 (mp0) REVERT: A 38 LYS cc_start: 0.7533 (mttm) cc_final: 0.7128 (ttmm) REVERT: A 74 LYS cc_start: 0.6757 (tptp) cc_final: 0.6260 (ttpp) REVERT: B 1 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7917 (ptp) REVERT: C 47 TYR cc_start: 0.5743 (OUTLIER) cc_final: 0.4766 (m-80) REVERT: C 118 GLU cc_start: 0.6497 (tm-30) cc_final: 0.5628 (tt0) REVERT: C 175 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7980 (tttm) REVERT: C 431 ILE cc_start: 0.7139 (mm) cc_final: 0.6895 (mt) REVERT: D 112 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7297 (tm-30) REVERT: D 373 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7289 (tp30) REVERT: E 149 TYR cc_start: 0.7839 (t80) cc_final: 0.7636 (t80) REVERT: E 228 MET cc_start: 0.7938 (ptp) cc_final: 0.7635 (ptm) REVERT: E 389 GLU cc_start: 0.6926 (tt0) cc_final: 0.6500 (tp30) REVERT: E 392 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6754 (mm-30) REVERT: E 414 TRP cc_start: 0.7487 (m-90) cc_final: 0.6754 (m-90) REVERT: F 181 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7145 (ttmm) REVERT: F 399 GLN cc_start: 0.6969 (OUTLIER) cc_final: 0.6676 (tp40) REVERT: H 80 GLU cc_start: 0.7854 (mm-30) cc_final: 0.6648 (mp0) REVERT: H 94 ARG cc_start: 0.7621 (mmm-85) cc_final: 0.7165 (mmm160) REVERT: H 130 LEU cc_start: 0.2568 (mp) cc_final: 0.2208 (mt) REVERT: H 158 GLU cc_start: 0.3293 (OUTLIER) cc_final: 0.2873 (pm20) REVERT: H 244 ASN cc_start: 0.6896 (m-40) cc_final: 0.6484 (t0) REVERT: H 281 MET cc_start: 0.7753 (mmt) cc_final: 0.7297 (mmm) REVERT: H 295 ASP cc_start: 0.6542 (p0) cc_final: 0.5959 (p0) outliers start: 85 outliers final: 66 residues processed: 381 average time/residue: 0.1556 time to fit residues: 93.5072 Evaluate side-chains 369 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 296 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 356 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 1 MET 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 270 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 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 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 56 LEU Chi-restraints excluded: chain D residue 90 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 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 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 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 F residue 2 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 166 MET 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 368 MET Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 404 ILE 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: 0.1980 chunk 63 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 252 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 166 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 247 optimal weight: 9.9990 chunk 143 optimal weight: 10.0000 chunk 237 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.146145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.120995 restraints weight = 39331.640| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.05 r_work: 0.3395 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 24197 Z= 0.155 Angle : 0.575 10.250 32807 Z= 0.305 Chirality : 0.043 0.237 3647 Planarity : 0.004 0.042 4071 Dihedral : 10.594 168.429 3351 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.17 % Allowed : 15.50 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.16), residues: 2898 helix: 1.21 (0.14), residues: 1456 sheet: -0.46 (0.26), residues: 405 loop : -1.46 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 124 TYR 0.026 0.001 TYR H 86 PHE 0.015 0.002 PHE H 81 TRP 0.022 0.001 TRP H 150 HIS 0.007 0.001 HIS H 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (24197) covalent geometry : angle 0.57515 / 0.30 (32807) hydrogen bonds : bond 0.03607 / 2.45 ( 1158) hydrogen bonds : angle 4.80904 / 3.45 ( 3303) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 308 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7826 (mp0) cc_final: 0.7534 (mp0) REVERT: A 38 LYS cc_start: 0.7451 (mttm) cc_final: 0.7119 (ttmm) REVERT: A 74 LYS cc_start: 0.6624 (tptp) cc_final: 0.6230 (ttmm) REVERT: B 1 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7830 (ptp) REVERT: C 47 TYR cc_start: 0.5614 (OUTLIER) cc_final: 0.5053 (m-10) REVERT: C 118 GLU cc_start: 0.6333 (tm-30) cc_final: 0.5494 (tt0) REVERT: C 142 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7408 (mt) REVERT: C 175 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7897 (tttm) REVERT: D 112 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7058 (tm-30) REVERT: D 134 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7517 (mt) REVERT: D 373 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7110 (tp30) REVERT: E 392 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6725 (mm-30) REVERT: E 414 TRP cc_start: 0.7361 (m-90) cc_final: 0.6241 (m-90) REVERT: F 181 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7077 (ttmm) REVERT: F 243 ASP cc_start: 0.7169 (m-30) cc_final: 0.6894 (t0) REVERT: F 326 GLU cc_start: 0.5953 (mt-10) cc_final: 0.5576 (mt-10) REVERT: F 399 GLN cc_start: 0.6994 (OUTLIER) cc_final: 0.6733 (tp40) REVERT: H 80 GLU cc_start: 0.7809 (mm-30) cc_final: 0.6650 (mp0) REVERT: H 94 ARG cc_start: 0.7468 (mmm-85) cc_final: 0.7001 (mmm160) REVERT: H 158 GLU cc_start: 0.3353 (OUTLIER) cc_final: 0.2891 (pm20) REVERT: H 194 PHE cc_start: 0.3373 (p90) cc_final: 0.2916 (p90) REVERT: H 244 ASN cc_start: 0.6841 (m-40) cc_final: 0.6102 (t0) REVERT: H 281 MET cc_start: 0.7613 (mmt) cc_final: 0.7180 (mmm) REVERT: H 295 ASP cc_start: 0.6397 (p0) cc_final: 0.5783 (p0) outliers start: 80 outliers final: 54 residues processed: 369 average time/residue: 0.1504 time to fit residues: 87.6838 Evaluate side-chains 358 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 295 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 356 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 1 MET 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 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 366 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 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 56 LEU Chi-restraints excluded: chain D residue 90 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 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 D residue 432 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 66 THR Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 244 VAL 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 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 368 MET Chi-restraints excluded: chain F residue 399 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 116 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 276 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 56 optimal weight: 0.5980 chunk 112 optimal weight: 9.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 200 ASN B 399 GLN D 167 ASN ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN F 200 ASN H 252 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.144940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.119727 restraints weight = 39593.819| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.09 r_work: 0.3377 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24197 Z= 0.174 Angle : 0.594 10.770 32807 Z= 0.314 Chirality : 0.044 0.245 3647 Planarity : 0.004 0.040 4071 Dihedral : 10.669 166.138 3351 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.09 % Allowed : 15.54 % Favored : 81.37 % 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: -0.03 (0.16), residues: 2898 helix: 1.15 (0.14), residues: 1458 sheet: -0.41 (0.27), residues: 398 loop : -1.53 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 340 TYR 0.024 0.002 TYR D 158 PHE 0.022 0.002 PHE D 146 TRP 0.019 0.002 TRP H 159 HIS 0.007 0.001 HIS H 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (24197) covalent geometry : angle 0.59404 / 0.31 (32807) hydrogen bonds : bond 0.03726 / 2.52 ( 1158) hydrogen bonds : angle 4.84315 / 3.47 ( 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 374 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 296 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7799 (mp0) cc_final: 0.7528 (mp0) REVERT: A 38 LYS cc_start: 0.7471 (mttm) cc_final: 0.7139 (ttmm) REVERT: A 74 LYS cc_start: 0.6669 (tptp) cc_final: 0.6194 (ttmm) REVERT: C 47 TYR cc_start: 0.5669 (OUTLIER) cc_final: 0.5055 (m-10) REVERT: C 118 GLU cc_start: 0.6267 (tm-30) cc_final: 0.5446 (tt0) REVERT: C 142 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7277 (mt) REVERT: C 175 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7927 (tttm) REVERT: D 112 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7086 (tm-30) REVERT: D 134 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7542 (mt) REVERT: D 373 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7181 (tp30) REVERT: E 392 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6780 (mm-30) REVERT: E 414 TRP cc_start: 0.7390 (m-90) cc_final: 0.6257 (m-90) REVERT: F 181 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7174 (ttmm) REVERT: F 243 ASP cc_start: 0.7174 (m-30) cc_final: 0.6878 (t0) REVERT: F 326 GLU cc_start: 0.5965 (mt-10) cc_final: 0.5588 (mt-10) REVERT: F 399 GLN cc_start: 0.6975 (OUTLIER) cc_final: 0.6707 (tp40) REVERT: H 80 GLU cc_start: 0.7800 (mm-30) cc_final: 0.6660 (mp0) REVERT: H 94 ARG cc_start: 0.7410 (mmm-85) cc_final: 0.6947 (mmm160) REVERT: H 130 LEU cc_start: 0.1923 (mt) cc_final: 0.1699 (mt) REVERT: H 158 GLU cc_start: 0.3190 (OUTLIER) cc_final: 0.2722 (pm20) REVERT: H 244 ASN cc_start: 0.6739 (m-40) cc_final: 0.6093 (t0) REVERT: H 281 MET cc_start: 0.7627 (mmt) cc_final: 0.7212 (mmm) REVERT: H 295 ASP cc_start: 0.6430 (p0) cc_final: 0.6128 (p0) outliers start: 78 outliers final: 62 residues processed: 358 average time/residue: 0.1526 time to fit residues: 86.7590 Evaluate side-chains 366 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 296 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 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 144 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 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 366 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 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 56 LEU Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 90 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 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 230 GLU Chi-restraints excluded: chain E residue 244 VAL 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 131 VAL 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 368 MET Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 404 ILE 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 314 THR 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: 6.9990 chunk 56 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 179 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 chunk 241 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 184 optimal weight: 20.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 200 ASN B 399 GLN D 167 ASN ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.146050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121389 restraints weight = 39451.365| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.04 r_work: 0.3399 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4650 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= 0.135 Angle : 0.569 8.775 32807 Z= 0.301 Chirality : 0.043 0.237 3647 Planarity : 0.004 0.044 4071 Dihedral : 10.620 167.903 3351 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.70 % Allowed : 16.17 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.16), residues: 2898 helix: 1.24 (0.14), residues: 1460 sheet: -0.45 (0.27), residues: 401 loop : -1.50 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 124 TYR 0.022 0.001 TYR H 86 PHE 0.018 0.002 PHE H 194 TRP 0.021 0.001 TRP H 159 HIS 0.006 0.001 HIS H 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (24197) covalent geometry : angle 0.56854 / 0.30 (32807) hydrogen bonds : bond 0.03519 / 2.39 ( 1158) hydrogen bonds : angle 4.76409 / 3.41 ( 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 364 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 296 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8086 (mp0) cc_final: 0.7831 (mp0) REVERT: A 38 LYS cc_start: 0.7519 (mttm) cc_final: 0.7118 (ttmm) REVERT: A 74 LYS cc_start: 0.6623 (tptp) cc_final: 0.6168 (ttmm) REVERT: A 76 LEU cc_start: 0.7766 (tp) cc_final: 0.7398 (mt) REVERT: B 391 GLU cc_start: 0.7401 (tp30) cc_final: 0.7074 (tp30) REVERT: C 47 TYR cc_start: 0.5768 (OUTLIER) cc_final: 0.5173 (m-10) REVERT: C 118 GLU cc_start: 0.6359 (tm-30) cc_final: 0.5562 (tt0) REVERT: C 142 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7247 (mt) REVERT: C 175 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8002 (tttm) REVERT: D 112 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7374 (tm-30) REVERT: D 134 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7624 (mt) REVERT: D 167 ASN cc_start: 0.6148 (OUTLIER) cc_final: 0.5888 (t0) REVERT: D 373 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7295 (tp30) REVERT: E 228 MET cc_start: 0.8013 (ptp) cc_final: 0.7696 (ptt) REVERT: E 392 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6853 (mm-30) REVERT: E 414 TRP cc_start: 0.7477 (m-90) cc_final: 0.6301 (m-90) REVERT: F 181 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7179 (ttmm) REVERT: F 243 ASP cc_start: 0.7372 (m-30) cc_final: 0.6978 (t0) REVERT: F 326 GLU cc_start: 0.6173 (mt-10) cc_final: 0.5812 (mt-10) REVERT: F 399 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.6740 (tp40) REVERT: H 80 GLU cc_start: 0.7734 (mm-30) cc_final: 0.6616 (mp0) REVERT: H 94 ARG cc_start: 0.7434 (mmm-85) cc_final: 0.6990 (mmm160) REVERT: H 130 LEU cc_start: 0.1932 (mt) cc_final: 0.1718 (mt) REVERT: H 158 GLU cc_start: 0.3349 (OUTLIER) cc_final: 0.2945 (pm20) REVERT: H 244 ASN cc_start: 0.6778 (m-40) cc_final: 0.6104 (t0) REVERT: H 281 MET cc_start: 0.7732 (mmt) cc_final: 0.7300 (mmm) REVERT: H 295 ASP cc_start: 0.6472 (p0) cc_final: 0.5889 (p0) outliers start: 68 outliers final: 53 residues processed: 349 average time/residue: 0.1553 time to fit residues: 85.5081 Evaluate side-chains 344 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 282 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU 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 144 ILE Chi-restraints excluded: chain B residue 163 LEU 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 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 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 56 LEU Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 167 ASN 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 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 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 368 MET Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain H residue 158 GLU 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 314 THR 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: 3.9990 chunk 12 optimal weight: 0.9980 chunk 142 optimal weight: 8.9990 chunk 102 optimal weight: 0.0040 chunk 96 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 273 optimal weight: 10.0000 chunk 226 optimal weight: 4.9990 chunk 251 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 200 ASN ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 252 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.146417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.121705 restraints weight = 39341.817| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.07 r_work: 0.3403 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.202 24197 Z= 0.190 Angle : 0.805 59.022 32807 Z= 0.487 Chirality : 0.044 0.740 3647 Planarity : 0.004 0.072 4071 Dihedral : 10.620 167.908 3351 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.66 % Allowed : 16.17 % Favored : 81.17 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.16), residues: 2898 helix: 1.24 (0.14), residues: 1460 sheet: -0.45 (0.27), residues: 401 loop : -1.52 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 124 TYR 0.020 0.001 TYR H 86 PHE 0.019 0.002 PHE H 194 TRP 0.044 0.002 TRP F 428 HIS 0.005 0.001 HIS H 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 (24197) covalent geometry : angle 0.80460 / 0.49 (32807) hydrogen bonds : bond 0.03513 / 2.39 ( 1158) hydrogen bonds : angle 4.76286 / 3.41 ( 3303) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5356.76 seconds wall clock time: 92 minutes 59.04 seconds (5579.04 seconds total)