Starting phenix.real_space_refine on Sun Aug 24 23:07:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dvf_27737/08_2025/8dvf_27737.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dvf_27737/08_2025/8dvf_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 { model { file = "/net/cci-nas-00/data/ceres_data/8dvf_27737/08_2025/8dvf_27737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dvf_27737/08_2025/8dvf_27737.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dvf_27737/08_2025/8dvf_27737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dvf_27737/08_2025/8dvf_27737.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23693 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "B" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "C" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "D" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "E" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "F" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "M" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "H" Number of atoms: 2644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2644 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain breaks: 1 Chain: "T" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.09, per 1000 atoms: 0.21 Number of scatterers: 23693 At special positions: 0 Unit cell: (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: 1.78 Conformation dependent library (CDL) restraints added in 876.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5530 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 20 sheets defined 53.9% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 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: 3.87 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 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: 32336 2.51 - 5.01: 435 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=" N ASP A 82 " pdb=" CA ASP A 82 " pdb=" C ASP A 82 " ideal model delta sigma weight residual 112.57 108.09 4.48 1.13e+00 7.83e-01 1.57e+01 angle pdb=" CA PHE D 383 " pdb=" CB PHE D 383 " pdb=" CG PHE D 383 " ideal model delta sigma weight residual 113.80 117.73 -3.93 1.00e+00 1.00e+00 1.55e+01 angle pdb=" C GLY F 151 " pdb=" N HIS F 152 " pdb=" CA HIS F 152 " ideal model delta sigma weight residual 122.30 117.08 5.22 1.35e+00 5.49e-01 1.49e+01 ... (remaining 32802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 14414 35.65 - 71.31: 203 71.31 - 106.96: 9 106.96 - 142.61: 1 142.61 - 178.27: 4 Dihedral angle restraints: 14631 sinusoidal: 6069 harmonic: 8562 Sorted by residual: dihedral pdb=" O1B AGS E 501 " pdb=" O3B AGS E 501 " pdb=" PB AGS E 501 " pdb=" PG AGS E 501 " ideal model delta sinusoidal sigma weight residual 68.91 -112.82 -178.27 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A AGS F 501 " pdb=" O3A AGS F 501 " pdb=" PA AGS F 501 " pdb=" PB AGS F 501 " ideal model delta sinusoidal sigma weight residual -67.73 106.44 -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 14628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2726 0.047 - 0.093: 622 0.093 - 0.140: 242 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: 2.200 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: 0.250 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.850 Find NCS groups from input model: 0.350 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 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= 0.300 Angle : 0.682 12.535 32807 Z= 0.443 Chirality : 0.049 0.233 3647 Planarity : 0.004 0.075 4071 Dihedral : 12.507 178.268 9101 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 aren 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 covalent geometry : bond 0.00440 (24197) covalent geometry : angle 0.68184 (32807) hydrogen bonds : bond 0.15940 ( 1158) hydrogen bonds : angle 6.57971 ( 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 : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 TYR cc_start: 0.7889 (m-80) cc_final: 0.7365 (m-80) REVERT: A 47 TYR cc_start: 0.6915 (m-10) cc_final: 0.6704 (m-10) REVERT: A 104 PHE cc_start: 0.7783 (t80) cc_final: 0.7431 (t80) REVERT: A 150 VAL cc_start: 0.8809 (t) cc_final: 0.8597 (m) REVERT: A 164 SER cc_start: 0.8518 (m) cc_final: 0.8224 (t) REVERT: A 228 MET cc_start: 0.6399 (mtp) cc_final: 0.5939 (mtp) REVERT: A 292 SER cc_start: 0.7262 (p) cc_final: 0.7024 (t) REVERT: A 333 LYS cc_start: 0.5793 (OUTLIER) cc_final: 0.5552 (tttp) REVERT: B 66 THR cc_start: 0.6091 (p) cc_final: 0.5696 (m) REVERT: B 150 VAL cc_start: 0.8593 (t) cc_final: 0.8332 (p) REVERT: B 299 LEU cc_start: 0.8502 (mt) cc_final: 0.8068 (mt) REVERT: B 312 TYR cc_start: 0.5027 (t80) cc_final: 0.4790 (t80) REVERT: C 85 GLU cc_start: 0.5980 (mm-30) cc_final: 0.5749 (mm-30) REVERT: C 150 VAL cc_start: 0.7503 (p) cc_final: 0.7095 (p) REVERT: C 157 ASP cc_start: 0.7634 (m-30) cc_final: 0.7303 (m-30) REVERT: C 263 MET cc_start: 0.8289 (mmm) cc_final: 0.8036 (mmp) REVERT: C 312 TYR cc_start: 0.4659 (t80) cc_final: 0.4421 (t80) REVERT: C 324 TYR cc_start: 0.7816 (m-80) cc_final: 0.7609 (m-80) REVERT: D 103 MET cc_start: 0.7495 (mmm) cc_final: 0.7255 (mtp) REVERT: D 293 LEU cc_start: 0.8466 (tp) cc_final: 0.8196 (tt) REVERT: D 384 MET cc_start: 0.8386 (mtm) cc_final: 0.8127 (mtm) REVERT: E 344 VAL cc_start: 0.7064 (p) cc_final: 0.6844 (m) REVERT: E 392 GLU cc_start: 0.6637 (mt-10) cc_final: 0.6217 (mm-30) REVERT: E 414 TRP cc_start: 0.7134 (m-90) cc_final: 0.6525 (m-90) REVERT: F 233 CYS cc_start: 0.7658 (m) cc_final: 0.7419 (m) REVERT: F 279 GLN cc_start: 0.7377 (tt0) cc_final: 0.7072 (tt0) REVERT: F 303 PHE cc_start: 0.8055 (t80) cc_final: 0.7852 (t80) REVERT: F 311 ASP cc_start: 0.7476 (t0) cc_final: 0.6696 (p0) REVERT: F 399 GLN cc_start: 0.6490 (OUTLIER) cc_final: 0.5586 (mt0) REVERT: F 418 LEU cc_start: 0.6114 (OUTLIER) cc_final: 0.5884 (tt) REVERT: F 430 GLU cc_start: 0.5715 (mt-10) cc_final: 0.5416 (tt0) REVERT: H 35 PHE cc_start: 0.4147 (p90) cc_final: 0.3923 (p90) REVERT: H 80 GLU cc_start: 0.5633 (mm-30) cc_final: 0.4519 (pt0) REVERT: H 88 GLU cc_start: 0.6975 (pt0) cc_final: 0.6582 (pm20) REVERT: H 89 TYR cc_start: 0.6084 (t80) cc_final: 0.5848 (t80) REVERT: H 213 TYR cc_start: 0.4202 (p90) cc_final: 0.3856 (p90) REVERT: H 225 VAL cc_start: 0.5885 (t) cc_final: 0.5645 (t) REVERT: H 234 GLU cc_start: 0.5461 (mt-10) cc_final: 0.4966 (mt-10) REVERT: H 244 ASN cc_start: 0.5804 (m-40) cc_final: 0.5280 (t0) REVERT: H 254 ASP cc_start: 0.4001 (t0) cc_final: 0.3725 (t70) REVERT: H 264 ARG cc_start: 0.5244 (ptt180) cc_final: 0.4731 (ptt180) REVERT: H 270 ASN cc_start: 0.6320 (t0) cc_final: 0.6112 (t0) REVERT: H 276 ASP cc_start: 0.6781 (m-30) cc_final: 0.6503 (m-30) REVERT: H 278 ILE cc_start: 0.6903 (pp) cc_final: 0.6483 (mm) REVERT: H 281 MET cc_start: 0.6844 (mmt) cc_final: 0.6395 (mmm) REVERT: H 289 GLU cc_start: 0.6628 (mm-30) cc_final: 0.5611 (mm-30) REVERT: H 293 PHE cc_start: 0.6403 (m-80) cc_final: 0.5795 (m-80) REVERT: H 322 MET cc_start: 0.6755 (mtm) cc_final: 0.6542 (mtm) outliers start: 45 outliers final: 7 residues processed: 794 average time/residue: 0.1637 time to fit residues: 194.6725 Evaluate side-chains 394 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 384 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain H residue 334 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 116 ASN A 327 ASN A 403 GLN B 200 ASN B 355 GLN B 399 GLN C 8 HIS D 116 ASN D 167 ASN 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 = 0.3974 r_free = 0.3974 target = 0.151505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.126445 restraints weight = 39575.549| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.15 r_work: 0.3472 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24197 Z= 0.154 Angle : 0.588 7.281 32807 Z= 0.316 Chirality : 0.043 0.186 3647 Planarity : 0.004 0.058 4071 Dihedral : 10.780 169.105 3418 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.62 % Allowed : 12.17 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.16), residues: 2898 helix: 1.33 (0.14), residues: 1456 sheet: -0.41 (0.26), residues: 421 loop : -1.13 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 124 TYR 0.020 0.002 TYR F 15 PHE 0.016 0.002 PHE H 11 TRP 0.020 0.001 TRP H 266 HIS 0.009 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00348 (24197) covalent geometry : angle 0.58827 (32807) hydrogen bonds : bond 0.04191 ( 1158) hydrogen bonds : angle 5.15628 ( 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 471 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 405 time to evaluate : 0.608 Fit side-chains REVERT: A 19 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.8202 (t) REVERT: A 22 TYR cc_start: 0.7938 (m-80) cc_final: 0.7421 (m-80) REVERT: A 38 LYS cc_start: 0.7517 (mttm) cc_final: 0.6974 (ttmm) REVERT: A 47 TYR cc_start: 0.7367 (m-10) cc_final: 0.7160 (m-10) REVERT: A 178 ILE cc_start: 0.7764 (tp) cc_final: 0.7474 (tp) REVERT: C 85 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6510 (mm-30) REVERT: C 157 ASP cc_start: 0.7744 (m-30) cc_final: 0.7452 (m-30) REVERT: D 103 MET cc_start: 0.7148 (mmm) cc_final: 0.6931 (mtp) REVERT: D 264 GLU cc_start: 0.6582 (mm-30) cc_final: 0.6357 (mm-30) REVERT: E 228 MET cc_start: 0.7478 (mtm) cc_final: 0.7230 (ptm) REVERT: E 392 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6277 (mm-30) REVERT: E 414 TRP cc_start: 0.7282 (m-90) cc_final: 0.6652 (m-90) REVERT: F 311 ASP cc_start: 0.7428 (t0) cc_final: 0.6786 (p0) REVERT: F 418 LEU cc_start: 0.6063 (OUTLIER) cc_final: 0.5726 (tt) REVERT: H 80 GLU cc_start: 0.7666 (mm-30) cc_final: 0.5901 (pt0) REVERT: H 244 ASN cc_start: 0.6646 (m-40) cc_final: 0.6344 (t0) REVERT: H 264 ARG cc_start: 0.6833 (ptt180) cc_final: 0.6134 (ptt180) REVERT: H 278 ILE cc_start: 0.8392 (pp) cc_final: 0.7893 (mm) REVERT: H 281 MET cc_start: 0.7679 (mmt) cc_final: 0.7135 (mmm) REVERT: H 307 MET cc_start: 0.6732 (mtm) cc_final: 0.6223 (mtp) outliers start: 66 outliers final: 40 residues processed: 452 average time/residue: 0.1465 time to fit residues: 104.6584 Evaluate side-chains 357 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 315 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 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 366 VAL Chi-restraints excluded: chain C residue 404 ILE 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 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 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 346 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 285 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 85 optimal weight: 8.9990 chunk 248 optimal weight: 0.7980 chunk 150 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 178 optimal weight: 9.9990 chunk 154 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 ASN B 355 GLN C 35 ASN D 114 GLN D 167 ASN D 399 GLN E 403 GLN F 216 GLN H 195 GLN H 325 ASN H 328 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.149587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.124347 restraints weight = 39378.426| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.13 r_work: 0.3438 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24197 Z= 0.146 Angle : 0.555 7.116 32807 Z= 0.297 Chirality : 0.043 0.244 3647 Planarity : 0.004 0.070 4071 Dihedral : 10.598 162.934 3411 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.54 % Allowed : 13.87 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.16), residues: 2898 helix: 1.35 (0.14), residues: 1454 sheet: -0.33 (0.27), residues: 408 loop : -1.20 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 94 TYR 0.019 0.001 TYR F 15 PHE 0.012 0.002 PHE D 65 TRP 0.018 0.001 TRP A 361 HIS 0.005 0.001 HIS H 274 Details of bonding type rmsd covalent geometry : bond 0.00330 (24197) covalent geometry : angle 0.55516 (32807) hydrogen bonds : bond 0.03832 ( 1158) hydrogen bonds : angle 4.88105 ( 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 408 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 344 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 19 VAL cc_start: 0.8424 (OUTLIER) cc_final: 0.8111 (t) REVERT: A 38 LYS cc_start: 0.7521 (mttm) cc_final: 0.7031 (ttmm) REVERT: A 380 THR cc_start: 0.7207 (OUTLIER) cc_final: 0.6964 (m) REVERT: C 85 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6806 (mm-30) REVERT: C 118 GLU cc_start: 0.6409 (tm-30) cc_final: 0.5631 (tt0) REVERT: C 139 ARG cc_start: 0.6990 (mtm-85) cc_final: 0.6769 (mtm-85) REVERT: C 157 ASP cc_start: 0.7860 (m-30) cc_final: 0.7599 (m-30) REVERT: D 103 MET cc_start: 0.7268 (mmm) cc_final: 0.7040 (mtp) REVERT: E 392 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6471 (mm-30) REVERT: E 414 TRP cc_start: 0.7275 (m-90) cc_final: 0.6204 (m-90) REVERT: F 311 ASP cc_start: 0.7579 (t0) cc_final: 0.7296 (t0) REVERT: F 321 ILE cc_start: 0.7219 (mt) cc_final: 0.6221 (mt) REVERT: F 399 GLN cc_start: 0.6787 (OUTLIER) cc_final: 0.6359 (tp40) REVERT: F 418 LEU cc_start: 0.6042 (OUTLIER) cc_final: 0.5647 (tt) REVERT: H 80 GLU cc_start: 0.7793 (mm-30) cc_final: 0.6597 (tm-30) REVERT: H 213 TYR cc_start: 0.4385 (p90) cc_final: 0.4130 (p90) REVERT: H 244 ASN cc_start: 0.6683 (m-40) cc_final: 0.6390 (t0) REVERT: H 278 ILE cc_start: 0.8314 (pp) cc_final: 0.8033 (mm) REVERT: H 281 MET cc_start: 0.7676 (mmt) cc_final: 0.7160 (mmm) REVERT: H 307 MET cc_start: 0.6417 (mtm) cc_final: 0.6186 (mtp) outliers start: 64 outliers final: 41 residues processed: 387 average time/residue: 0.1526 time to fit residues: 92.3837 Evaluate side-chains 348 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 303 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 254 ILE 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 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 50 VAL Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 8 HIS 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 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: 10.0000 chunk 191 optimal weight: 6.9990 chunk 156 optimal weight: 0.8980 chunk 268 optimal weight: 8.9990 chunk 56 optimal weight: 0.6980 chunk 289 optimal weight: 5.9990 chunk 288 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 285 optimal weight: 0.2980 chunk 132 optimal weight: 7.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN D 167 ASN E 403 GLN H 188 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.147852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.122896 restraints weight = 39339.311| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.08 r_work: 0.3417 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3683 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= 0.157 Angle : 0.554 7.223 32807 Z= 0.297 Chirality : 0.043 0.263 3647 Planarity : 0.004 0.039 4071 Dihedral : 10.549 156.774 3409 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.49 % Allowed : 13.67 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.16), residues: 2898 helix: 1.32 (0.14), residues: 1449 sheet: -0.33 (0.27), residues: 405 loop : -1.29 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 124 TYR 0.015 0.001 TYR F 15 PHE 0.019 0.002 PHE D 146 TRP 0.011 0.001 TRP A 162 HIS 0.011 0.001 HIS D 152 Details of bonding type rmsd covalent geometry : bond 0.00362 (24197) covalent geometry : angle 0.55388 (32807) hydrogen bonds : bond 0.03682 ( 1158) hydrogen bonds : angle 4.80158 ( 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 429 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 341 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7509 (mttm) cc_final: 0.7092 (ttmm) REVERT: A 267 ARG cc_start: 0.7090 (ttm-80) cc_final: 0.6868 (ttp80) REVERT: A 345 GLU cc_start: 0.7985 (tp30) cc_final: 0.7737 (tp30) REVERT: A 380 THR cc_start: 0.7299 (OUTLIER) cc_final: 0.7049 (t) REVERT: A 417 PHE cc_start: 0.4846 (t80) cc_final: 0.4564 (t80) REVERT: C 85 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6859 (mm-30) REVERT: C 113 ILE cc_start: 0.8436 (mp) cc_final: 0.8235 (mp) REVERT: C 118 GLU cc_start: 0.6398 (tm-30) cc_final: 0.5602 (tt0) REVERT: C 128 MET cc_start: 0.6737 (mmm) cc_final: 0.6404 (mmm) REVERT: C 157 ASP cc_start: 0.7932 (m-30) cc_final: 0.7695 (m-30) REVERT: D 103 MET cc_start: 0.7286 (mmm) cc_final: 0.7072 (mtp) REVERT: D 134 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7690 (mt) REVERT: D 406 SER cc_start: 0.7687 (t) cc_final: 0.7468 (p) REVERT: E 228 MET cc_start: 0.7610 (mtm) cc_final: 0.7352 (ptm) REVERT: E 392 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6458 (mm-30) REVERT: E 414 TRP cc_start: 0.7342 (m-90) cc_final: 0.6145 (m-90) REVERT: F 181 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.6973 (ttmm) REVERT: F 399 GLN cc_start: 0.6686 (OUTLIER) cc_final: 0.6286 (tp40) REVERT: F 418 LEU cc_start: 0.6071 (OUTLIER) cc_final: 0.5597 (tt) REVERT: H 80 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7011 (mp0) REVERT: H 158 GLU cc_start: 0.3097 (OUTLIER) cc_final: 0.2874 (pm20) REVERT: H 244 ASN cc_start: 0.6728 (m-40) cc_final: 0.6387 (t0) REVERT: H 278 ILE cc_start: 0.8300 (pp) cc_final: 0.8042 (mm) REVERT: H 281 MET cc_start: 0.7633 (mmt) cc_final: 0.7144 (mmm) REVERT: H 307 MET cc_start: 0.6500 (mtm) cc_final: 0.6243 (mtp) outliers start: 88 outliers final: 57 residues processed: 406 average time/residue: 0.1471 time to fit residues: 93.8206 Evaluate side-chains 365 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 302 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 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 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 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 319 CYS Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 175 LYS Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 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 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 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 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 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: 2.9990 chunk 253 optimal weight: 3.9990 chunk 282 optimal weight: 0.0020 chunk 134 optimal weight: 9.9990 chunk 266 optimal weight: 7.9990 chunk 281 optimal weight: 9.9990 chunk 172 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 226 optimal weight: 8.9990 overall best weight: 3.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN B 200 ASN B 355 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN D 167 ASN ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN F 57 ASN F 116 ASN F 355 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.144654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.119944 restraints weight = 39417.372| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.08 r_work: 0.3368 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 24197 Z= 0.203 Angle : 0.625 8.448 32807 Z= 0.330 Chirality : 0.045 0.287 3647 Planarity : 0.004 0.039 4071 Dihedral : 10.720 157.381 3409 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.65 % Allowed : 14.78 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.16), residues: 2898 helix: 1.06 (0.14), residues: 1446 sheet: -0.54 (0.26), residues: 399 loop : -1.39 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 264 TYR 0.024 0.002 TYR D 158 PHE 0.021 0.002 PHE H 81 TRP 0.016 0.002 TRP F 428 HIS 0.006 0.002 HIS H 274 Details of bonding type rmsd covalent geometry : bond 0.00474 (24197) covalent geometry : angle 0.62541 (32807) hydrogen bonds : bond 0.04056 ( 1158) hydrogen bonds : angle 4.92228 ( 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 431 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 339 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7502 (mttm) cc_final: 0.7137 (ttmm) REVERT: A 74 LYS cc_start: 0.6888 (tptp) cc_final: 0.6325 (ttmm) REVERT: A 291 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.6923 (ttm-80) REVERT: A 355 GLN cc_start: 0.7407 (tp40) cc_final: 0.6538 (mm-40) REVERT: C 47 TYR cc_start: 0.5637 (OUTLIER) cc_final: 0.5009 (m-10) REVERT: C 74 LYS cc_start: 0.6854 (mmtt) cc_final: 0.6653 (mmmm) REVERT: C 113 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8380 (mp) REVERT: C 118 GLU cc_start: 0.6337 (tm-30) cc_final: 0.5538 (tt0) REVERT: C 128 MET cc_start: 0.6781 (mmm) cc_final: 0.6402 (mmm) REVERT: C 175 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7946 (tttm) REVERT: C 431 ILE cc_start: 0.7070 (mm) cc_final: 0.6848 (mt) REVERT: D 103 MET cc_start: 0.7212 (mmm) cc_final: 0.6970 (mtp) REVERT: D 112 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.6999 (tm-30) REVERT: D 167 ASN cc_start: 0.6058 (OUTLIER) cc_final: 0.5695 (t0) REVERT: D 175 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7759 (mtpt) REVERT: D 406 SER cc_start: 0.8141 (t) cc_final: 0.7675 (p) REVERT: E 389 GLU cc_start: 0.6914 (tt0) cc_final: 0.6450 (tp30) REVERT: E 392 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6760 (mm-30) REVERT: E 414 TRP cc_start: 0.7400 (m-90) cc_final: 0.6680 (m-90) REVERT: F 181 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7126 (ttmm) REVERT: F 243 ASP cc_start: 0.7215 (m-30) cc_final: 0.6896 (t0) REVERT: F 399 GLN cc_start: 0.6863 (OUTLIER) cc_final: 0.6623 (tp40) REVERT: H 80 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7256 (mp0) REVERT: H 158 GLU cc_start: 0.3055 (OUTLIER) cc_final: 0.2687 (pm20) REVERT: H 190 LYS cc_start: 0.6707 (pptt) cc_final: 0.5442 (ttmt) REVERT: H 244 ASN cc_start: 0.6783 (m-40) cc_final: 0.6153 (t0) REVERT: H 264 ARG cc_start: 0.6237 (ptt180) cc_final: 0.5992 (ptt90) REVERT: H 281 MET cc_start: 0.7686 (mmt) cc_final: 0.7275 (mmm) REVERT: H 295 ASP cc_start: 0.6686 (p0) cc_final: 0.6094 (p0) REVERT: H 307 MET cc_start: 0.6434 (mtm) cc_final: 0.6133 (mtp) REVERT: H 322 MET cc_start: 0.8423 (mtp) cc_final: 0.8214 (mtp) outliers start: 92 outliers final: 59 residues processed: 408 average time/residue: 0.1549 time to fit residues: 97.3471 Evaluate side-chains 364 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 295 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 291 ARG Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 50 VAL 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 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 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 145 SER Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 64 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 181 optimal weight: 3.9990 chunk 229 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 235 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 ASN D 114 GLN D 288 ASN ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 200 ASN F 398 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.145594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.120498 restraints weight = 39605.537| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.10 r_work: 0.3376 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24197 Z= 0.148 Angle : 0.562 7.799 32807 Z= 0.298 Chirality : 0.042 0.238 3647 Planarity : 0.004 0.040 4071 Dihedral : 10.575 158.025 3407 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.45 % Allowed : 15.50 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.16), residues: 2898 helix: 1.18 (0.14), residues: 1449 sheet: -0.50 (0.26), residues: 405 loop : -1.42 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 177 TYR 0.027 0.001 TYR H 86 PHE 0.016 0.002 PHE H 81 TRP 0.019 0.002 TRP H 150 HIS 0.005 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00341 (24197) covalent geometry : angle 0.56171 (32807) hydrogen bonds : bond 0.03653 ( 1158) hydrogen bonds : angle 4.78880 ( 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 401 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 314 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7514 (mttm) cc_final: 0.7216 (ttmm) REVERT: A 74 LYS cc_start: 0.6900 (tptp) cc_final: 0.6358 (ttmm) REVERT: A 355 GLN cc_start: 0.7434 (tp40) cc_final: 0.6450 (mm-40) REVERT: C 74 LYS cc_start: 0.6814 (mmtt) cc_final: 0.6541 (mmmm) REVERT: C 118 GLU cc_start: 0.6309 (tm-30) cc_final: 0.5579 (tt0) REVERT: C 175 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7931 (tttm) REVERT: C 431 ILE cc_start: 0.7085 (mm) cc_final: 0.6859 (mt) REVERT: D 103 MET cc_start: 0.7231 (mmm) cc_final: 0.6970 (mtp) REVERT: D 112 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7082 (tm-30) REVERT: D 167 ASN cc_start: 0.6123 (OUTLIER) cc_final: 0.5686 (t0) REVERT: D 406 SER cc_start: 0.8120 (t) cc_final: 0.7690 (p) REVERT: E 228 MET cc_start: 0.7732 (mtm) cc_final: 0.7388 (ptm) REVERT: E 392 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6755 (mm-30) REVERT: E 414 TRP cc_start: 0.7364 (m-90) cc_final: 0.6664 (m-90) REVERT: F 181 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7090 (ttmm) REVERT: F 243 ASP cc_start: 0.7169 (m-30) cc_final: 0.6901 (t0) REVERT: F 399 GLN cc_start: 0.6871 (OUTLIER) cc_final: 0.6558 (tp40) REVERT: F 418 LEU cc_start: 0.6365 (OUTLIER) cc_final: 0.5994 (tp) REVERT: H 80 GLU cc_start: 0.7905 (mm-30) cc_final: 0.6634 (mp0) REVERT: H 158 GLU cc_start: 0.3125 (OUTLIER) cc_final: 0.2725 (pm20) REVERT: H 190 LYS cc_start: 0.6758 (pptt) cc_final: 0.5380 (ttmt) REVERT: H 194 PHE cc_start: 0.3372 (p90) cc_final: 0.2931 (p90) REVERT: H 244 ASN cc_start: 0.6809 (m-40) cc_final: 0.6119 (t0) REVERT: H 281 MET cc_start: 0.7672 (mmt) cc_final: 0.7258 (mmm) REVERT: H 295 ASP cc_start: 0.6566 (p0) cc_final: 0.5916 (p0) outliers start: 87 outliers final: 58 residues processed: 379 average time/residue: 0.1422 time to fit residues: 84.5713 Evaluate side-chains 368 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 303 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 19 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 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 131 VAL Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 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 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 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 282 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 8 HIS 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 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 F residue 418 LEU Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 308 ILE 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: 0.9990 chunk 28 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 270 optimal weight: 3.9990 chunk 246 optimal weight: 10.0000 chunk 286 optimal weight: 6.9990 chunk 256 optimal weight: 20.0000 chunk 269 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 ASN D 167 ASN D 288 ASN ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.145256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.120283 restraints weight = 39470.458| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.16 r_work: 0.3376 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24197 Z= 0.162 Angle : 0.577 9.042 32807 Z= 0.304 Chirality : 0.043 0.236 3647 Planarity : 0.004 0.037 4071 Dihedral : 10.594 158.577 3407 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.33 % Allowed : 15.97 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.16), residues: 2898 helix: 1.15 (0.14), residues: 1455 sheet: -0.51 (0.26), residues: 404 loop : -1.48 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 264 TYR 0.026 0.001 TYR H 86 PHE 0.019 0.002 PHE H 81 TRP 0.015 0.002 TRP H 150 HIS 0.004 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00375 (24197) covalent geometry : angle 0.57686 (32807) hydrogen bonds : bond 0.03681 ( 1158) hydrogen bonds : angle 4.79821 ( 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 395 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 311 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7512 (mttm) cc_final: 0.7223 (ttmm) REVERT: A 69 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6331 (mp0) REVERT: A 74 LYS cc_start: 0.6939 (tptp) cc_final: 0.6357 (ttmm) REVERT: A 119 LEU cc_start: 0.5449 (OUTLIER) cc_final: 0.5028 (mp) REVERT: A 124 ARG cc_start: 0.5546 (ttm110) cc_final: 0.5048 (mtp-110) REVERT: B 391 GLU cc_start: 0.7334 (tp30) cc_final: 0.7020 (tp30) REVERT: C 74 LYS cc_start: 0.6812 (mmtt) cc_final: 0.6534 (mmmm) REVERT: C 118 GLU cc_start: 0.6203 (tm-30) cc_final: 0.5513 (tt0) REVERT: C 142 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7134 (mt) REVERT: C 175 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7947 (tttm) REVERT: C 431 ILE cc_start: 0.7104 (mm) cc_final: 0.6860 (mt) REVERT: D 103 MET cc_start: 0.7261 (mmm) cc_final: 0.6968 (mtp) REVERT: D 112 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7063 (tm-30) REVERT: E 228 MET cc_start: 0.7835 (mtm) cc_final: 0.7449 (ptm) REVERT: E 392 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6769 (mm-30) REVERT: E 414 TRP cc_start: 0.7394 (m-90) cc_final: 0.6701 (m-90) REVERT: F 181 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7177 (ttmm) REVERT: F 201 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8155 (p) REVERT: F 243 ASP cc_start: 0.7179 (m-30) cc_final: 0.6899 (t0) REVERT: F 247 ASP cc_start: 0.6629 (m-30) cc_final: 0.6384 (m-30) REVERT: F 399 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.6626 (tp40) REVERT: F 418 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.6071 (tp) REVERT: H 80 GLU cc_start: 0.7857 (mm-30) cc_final: 0.6682 (mp0) REVERT: H 158 GLU cc_start: 0.3260 (OUTLIER) cc_final: 0.2841 (pm20) REVERT: H 159 TRP cc_start: 0.3459 (t-100) cc_final: 0.2978 (t-100) REVERT: H 190 LYS cc_start: 0.6806 (pptt) cc_final: 0.5454 (ttmt) REVERT: H 244 ASN cc_start: 0.6727 (m-40) cc_final: 0.6112 (t0) REVERT: H 252 GLN cc_start: 0.4471 (OUTLIER) cc_final: 0.3801 (tm-30) REVERT: H 281 MET cc_start: 0.7664 (mmt) cc_final: 0.7273 (mmm) REVERT: H 295 ASP cc_start: 0.6534 (p0) cc_final: 0.5890 (p0) outliers start: 84 outliers final: 61 residues processed: 374 average time/residue: 0.1321 time to fit residues: 78.1333 Evaluate side-chains 369 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 297 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 119 LEU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 304 VAL 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 116 ASN 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 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 230 GLU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 8 HIS 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 201 VAL 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 F residue 418 LEU Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 252 GLN 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: 0.5980 chunk 63 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 252 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 166 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 247 optimal weight: 7.9990 chunk 143 optimal weight: 4.9990 chunk 237 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 ASN ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN F 200 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.145120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.120138 restraints weight = 39599.213| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.11 r_work: 0.3378 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24197 Z= 0.145 Angle : 0.565 11.076 32807 Z= 0.297 Chirality : 0.042 0.227 3647 Planarity : 0.004 0.036 4071 Dihedral : 10.569 159.016 3407 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.05 % Allowed : 16.17 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.16), residues: 2898 helix: 1.22 (0.14), residues: 1453 sheet: -0.47 (0.27), residues: 397 loop : -1.45 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 264 TYR 0.025 0.001 TYR H 86 PHE 0.016 0.002 PHE H 81 TRP 0.015 0.001 TRP D 89 HIS 0.004 0.001 HIS H 274 Details of bonding type rmsd covalent geometry : bond 0.00334 (24197) covalent geometry : angle 0.56524 (32807) hydrogen bonds : bond 0.03545 ( 1158) hydrogen bonds : angle 4.76201 ( 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 385 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 308 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7477 (mttm) cc_final: 0.7124 (ttmm) REVERT: A 69 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6220 (mp0) REVERT: A 74 LYS cc_start: 0.6951 (tptp) cc_final: 0.6364 (ttmm) REVERT: A 291 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.6852 (ttm-80) REVERT: A 355 GLN cc_start: 0.7317 (tp40) cc_final: 0.6328 (mm-40) REVERT: B 391 GLU cc_start: 0.7388 (tp30) cc_final: 0.7080 (tp30) REVERT: C 74 LYS cc_start: 0.6788 (mmtt) cc_final: 0.6501 (mmmm) REVERT: C 142 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7220 (mt) REVERT: C 175 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7946 (tttm) REVERT: D 103 MET cc_start: 0.7276 (mmm) cc_final: 0.6976 (mtp) REVERT: E 228 MET cc_start: 0.7809 (mtm) cc_final: 0.7437 (ptm) REVERT: E 392 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6768 (mm-30) REVERT: E 414 TRP cc_start: 0.7392 (m-90) cc_final: 0.6260 (m-90) REVERT: F 1 MET cc_start: 0.7860 (ptt) cc_final: 0.7095 (ptt) REVERT: F 181 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7201 (ttmm) REVERT: F 243 ASP cc_start: 0.7160 (m-30) cc_final: 0.6907 (t0) REVERT: F 247 ASP cc_start: 0.6525 (m-30) cc_final: 0.6318 (m-30) REVERT: F 340 ARG cc_start: 0.8118 (ttt-90) cc_final: 0.7872 (ttt-90) REVERT: F 399 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6684 (tp40) REVERT: F 418 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.6077 (tp) REVERT: H 80 GLU cc_start: 0.7764 (mm-30) cc_final: 0.6644 (mp0) REVERT: H 158 GLU cc_start: 0.3352 (OUTLIER) cc_final: 0.2951 (pm20) REVERT: H 159 TRP cc_start: 0.3158 (t-100) cc_final: 0.2820 (t-100) REVERT: H 190 LYS cc_start: 0.6841 (pptt) cc_final: 0.5497 (ttmt) REVERT: H 244 ASN cc_start: 0.6640 (m-40) cc_final: 0.6000 (t0) REVERT: H 281 MET cc_start: 0.7672 (mmt) cc_final: 0.7295 (mmm) outliers start: 77 outliers final: 63 residues processed: 367 average time/residue: 0.1348 time to fit residues: 77.5609 Evaluate side-chains 365 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 294 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 291 ARG Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 275 LEU 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 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 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 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 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 163 LEU Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 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 F residue 418 LEU Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain H residue 314 THR 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: 6.9990 chunk 207 optimal weight: 10.0000 chunk 83 optimal weight: 0.4980 chunk 161 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 276 optimal weight: 30.0000 chunk 121 optimal weight: 1.9990 chunk 179 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 HIS ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 GLN D 399 GLN ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.146393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.122028 restraints weight = 39605.243| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.11 r_work: 0.3405 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24197 Z= 0.117 Angle : 0.543 10.278 32807 Z= 0.286 Chirality : 0.041 0.205 3647 Planarity : 0.003 0.036 4071 Dihedral : 10.450 158.978 3407 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.66 % Allowed : 16.81 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.16), residues: 2898 helix: 1.34 (0.14), residues: 1460 sheet: -0.38 (0.27), residues: 397 loop : -1.43 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 124 TYR 0.025 0.001 TYR D 329 PHE 0.015 0.001 PHE C 104 TRP 0.028 0.001 TRP H 154 HIS 0.006 0.001 HIS H 134 Details of bonding type rmsd covalent geometry : bond 0.00263 (24197) covalent geometry : angle 0.54304 (32807) hydrogen bonds : bond 0.03308 ( 1158) hydrogen bonds : angle 4.65677 ( 3303) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 308 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7534 (mttm) cc_final: 0.7184 (ttmm) REVERT: A 69 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6221 (mp0) REVERT: A 74 LYS cc_start: 0.6932 (tptp) cc_final: 0.6318 (ttmm) REVERT: A 243 ASP cc_start: 0.8200 (m-30) cc_final: 0.7854 (m-30) REVERT: A 291 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.6996 (ttm-80) REVERT: A 355 GLN cc_start: 0.7324 (tp40) cc_final: 0.6567 (mm-40) REVERT: B 391 GLU cc_start: 0.7449 (tp30) cc_final: 0.7139 (tp30) REVERT: C 74 LYS cc_start: 0.6771 (mmtt) cc_final: 0.6485 (mmmm) REVERT: C 124 ARG cc_start: 0.6841 (ptp-110) cc_final: 0.6128 (mtm-85) REVERT: C 142 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7227 (mt) REVERT: C 175 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.8002 (tttm) REVERT: D 103 MET cc_start: 0.7453 (mmm) cc_final: 0.7131 (mtp) REVERT: D 406 SER cc_start: 0.8332 (t) cc_final: 0.7911 (p) REVERT: E 228 MET cc_start: 0.7854 (mtm) cc_final: 0.7441 (ptm) REVERT: E 392 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6828 (mm-30) REVERT: E 414 TRP cc_start: 0.7461 (m-90) cc_final: 0.6299 (m-90) REVERT: F 1 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7024 (ptt) REVERT: F 181 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7159 (ttmm) REVERT: F 243 ASP cc_start: 0.7369 (m-30) cc_final: 0.7037 (t0) REVERT: F 247 ASP cc_start: 0.6673 (m-30) cc_final: 0.6460 (m-30) REVERT: F 399 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6728 (tp40) REVERT: F 418 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6140 (tp) REVERT: H 80 GLU cc_start: 0.7690 (mm-30) cc_final: 0.6621 (mp0) REVERT: H 130 LEU cc_start: 0.2817 (mp) cc_final: 0.2263 (mt) REVERT: H 158 GLU cc_start: 0.3433 (OUTLIER) cc_final: 0.3002 (pm20) REVERT: H 190 LYS cc_start: 0.6858 (pptt) cc_final: 0.5520 (ttmt) REVERT: H 244 ASN cc_start: 0.6693 (m-40) cc_final: 0.6026 (t0) REVERT: H 252 GLN cc_start: 0.4474 (OUTLIER) cc_final: 0.3719 (tm-30) REVERT: H 281 MET cc_start: 0.7736 (mmt) cc_final: 0.7308 (mmm) outliers start: 67 outliers final: 50 residues processed: 358 average time/residue: 0.1308 time to fit residues: 73.1745 Evaluate side-chains 354 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 294 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 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 304 VAL 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 25 SER Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 196 MET 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 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 350 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 230 GLU 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 1 MET Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 8 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 68 THR 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 418 LEU Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 285 VAL 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: 4.9990 chunk 56 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 179 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 208 optimal weight: 2.9990 chunk 241 optimal weight: 9.9990 chunk 135 optimal weight: 0.2980 chunk 184 optimal weight: 10.0000 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 ASN B 200 ASN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.145044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.120284 restraints weight = 39767.531| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.03 r_work: 0.3379 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24197 Z= 0.172 Angle : 0.593 9.861 32807 Z= 0.312 Chirality : 0.043 0.255 3647 Planarity : 0.004 0.036 4071 Dihedral : 10.642 159.928 3406 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.54 % Allowed : 17.36 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.16), residues: 2898 helix: 1.23 (0.14), residues: 1441 sheet: -0.54 (0.26), residues: 402 loop : -1.38 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 264 TYR 0.027 0.002 TYR H 220 PHE 0.017 0.002 PHE D 37 TRP 0.018 0.002 TRP H 154 HIS 0.007 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00403 (24197) covalent geometry : angle 0.59327 (32807) hydrogen bonds : bond 0.03655 ( 1158) hydrogen bonds : angle 4.77741 ( 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: 64 poor density : 300 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7643 (mttm) cc_final: 0.7371 (ttmm) REVERT: A 69 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6281 (mp0) REVERT: A 74 LYS cc_start: 0.7020 (tptp) cc_final: 0.6451 (ttmm) REVERT: A 243 ASP cc_start: 0.8218 (m-30) cc_final: 0.7893 (m-30) REVERT: A 291 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.6923 (ttm-80) REVERT: A 355 GLN cc_start: 0.7350 (tp40) cc_final: 0.6612 (mm-40) REVERT: B 391 GLU cc_start: 0.7522 (tp30) cc_final: 0.7231 (tp30) REVERT: C 74 LYS cc_start: 0.6790 (mmtt) cc_final: 0.6507 (mmmm) REVERT: C 113 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8442 (mp) REVERT: C 124 ARG cc_start: 0.6835 (ptp-110) cc_final: 0.6159 (mtm-85) REVERT: C 142 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7317 (mt) REVERT: C 175 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8027 (tptt) REVERT: D 103 MET cc_start: 0.7503 (mmm) cc_final: 0.7211 (mtp) REVERT: D 175 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7999 (ttpt) REVERT: E 228 MET cc_start: 0.7996 (mtm) cc_final: 0.7695 (ptm) REVERT: E 389 GLU cc_start: 0.7045 (tt0) cc_final: 0.6660 (tp30) REVERT: E 392 GLU cc_start: 0.7389 (mt-10) cc_final: 0.6886 (mm-30) REVERT: E 413 LYS cc_start: 0.7661 (tppt) cc_final: 0.6955 (tptp) REVERT: E 414 TRP cc_start: 0.7505 (m-90) cc_final: 0.6312 (m-90) REVERT: F 1 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7134 (ptt) REVERT: F 181 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7269 (ttmm) REVERT: F 243 ASP cc_start: 0.7362 (m-30) cc_final: 0.7023 (t0) REVERT: F 247 ASP cc_start: 0.6697 (m-30) cc_final: 0.6490 (m-30) REVERT: F 274 ARG cc_start: 0.6684 (mtp180) cc_final: 0.6303 (ttp80) REVERT: F 399 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.6750 (tp40) REVERT: F 418 LEU cc_start: 0.6553 (OUTLIER) cc_final: 0.6057 (tp) REVERT: H 80 GLU cc_start: 0.7730 (mm-30) cc_final: 0.6651 (mp0) REVERT: H 158 GLU cc_start: 0.3320 (OUTLIER) cc_final: 0.2909 (pm20) REVERT: H 190 LYS cc_start: 0.6994 (pptt) cc_final: 0.5735 (mttt) REVERT: H 244 ASN cc_start: 0.6667 (m-40) cc_final: 0.6078 (t0) REVERT: H 252 GLN cc_start: 0.4378 (OUTLIER) cc_final: 0.3332 (tm-30) REVERT: H 274 HIS cc_start: 0.7141 (t-170) cc_final: 0.6784 (t-170) REVERT: H 281 MET cc_start: 0.7794 (mmt) cc_final: 0.7391 (mmm) REVERT: H 295 ASP cc_start: 0.6631 (p0) cc_final: 0.6065 (p0) outliers start: 64 outliers final: 46 residues processed: 348 average time/residue: 0.1322 time to fit residues: 72.0633 Evaluate side-chains 349 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 291 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 291 ARG 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 200 ASN Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 275 LEU 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 366 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 113 ILE 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 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 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 350 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 230 GLU 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 1 MET 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 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 418 LEU Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 252 GLN 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: 9.9990 chunk 12 optimal weight: 0.0670 chunk 142 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 273 optimal weight: 9.9990 chunk 226 optimal weight: 5.9990 chunk 251 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 overall best weight: 1.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 ASN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.144881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.120051 restraints weight = 39631.340| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.15 r_work: 0.3371 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.205 24197 Z= 0.226 Angle : 0.735 59.195 32807 Z= 0.422 Chirality : 0.048 1.211 3647 Planarity : 0.004 0.035 4071 Dihedral : 10.639 159.900 3406 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.58 % Allowed : 17.20 % Favored : 80.22 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.16), residues: 2898 helix: 1.23 (0.14), residues: 1441 sheet: -0.54 (0.26), residues: 402 loop : -1.40 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 264 TYR 0.024 0.002 TYR H 220 PHE 0.016 0.002 PHE D 37 TRP 0.017 0.002 TRP H 154 HIS 0.005 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00482 (24197) covalent geometry : angle 0.73528 (32807) hydrogen bonds : bond 0.03633 ( 1158) hydrogen bonds : angle 4.77609 ( 3303) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4598.74 seconds wall clock time: 80 minutes 0.06 seconds (4800.06 seconds total)