Starting phenix.real_space_refine on Fri Jun 20 09:21:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dvi_27739/06_2025/8dvi_27739.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dvi_27739/06_2025/8dvi_27739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dvi_27739/06_2025/8dvi_27739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dvi_27739/06_2025/8dvi_27739.map" model { file = "/net/cci-nas-00/data/ceres_data/8dvi_27739/06_2025/8dvi_27739.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dvi_27739/06_2025/8dvi_27739.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 32 5.49 5 Mg 5 5.21 5 S 132 5.16 5 C 14995 2.51 5 N 3943 2.21 5 O 4586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.61, per 1000 atoms: 0.57 Number of scatterers: 23693 At special positions: 0 Unit cell: (134.136, 130.824, 142.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 132 16.00 P 32 15.00 Mg 5 11.99 O 4586 8.00 N 3943 7.00 C 14995 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.64 Conformation dependent library (CDL) restraints added in 2.8 seconds 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5530 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 20 sheets defined 53.8% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 Processing helix chain 'A' and resid 13 through 20 Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 24 through 28 Processing helix chain 'A' and resid 31 through 47 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 66 through 79 Processing helix chain 'A' and resid 86 through 118 Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 176 through 183 Processing helix chain 'A' and resid 202 through 217 removed outlier: 4.527A pdb=" N GLY A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 243 Processing helix chain 'A' and resid 245 through 252 removed outlier: 3.520A pdb=" N ILE A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 269 removed outlier: 3.550A pdb=" N LYS A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 301 Processing helix chain 'A' and resid 328 through 347 Processing helix chain 'A' and resid 357 through 363 Processing helix chain 'A' and resid 390 through 396 Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'B' and resid 12 through 20 Processing helix chain 'B' and resid 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 24 through 28 removed outlier: 3.542A pdb=" N TYR B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE B 28 " --> pdb=" O SER B 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 24 through 28' Processing helix chain 'B' and resid 31 through 48 Processing helix chain 'B' and resid 52 through 58 Processing helix chain 'B' and resid 66 through 80 Processing helix chain 'B' and resid 88 through 119 removed outlier: 3.529A pdb=" N LEU B 119 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 133 Processing helix chain 'B' and resid 134 through 143 Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 176 through 184 removed outlier: 3.512A pdb=" N ILE B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 217 Processing helix chain 'B' and resid 229 through 243 removed outlier: 3.568A pdb=" N ASP B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 Processing helix chain 'B' and resid 255 through 269 removed outlier: 3.842A pdb=" N LYS B 269 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 301 Processing helix chain 'B' and resid 327 through 347 removed outlier: 3.589A pdb=" N THR B 331 " --> pdb=" O ASN B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'B' and resid 391 through 396 removed outlier: 3.628A pdb=" N ALA B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 13 through 20 Processing helix chain 'C' and resid 24 through 28 removed outlier: 3.769A pdb=" N PHE C 28 " --> pdb=" O SER C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 47 Processing helix chain 'C' and resid 52 through 63 Processing helix chain 'C' and resid 66 through 77 removed outlier: 4.001A pdb=" N GLY C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 119 Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 133 through 143 Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 203 through 217 Processing helix chain 'C' and resid 229 through 242 Processing helix chain 'C' and resid 245 through 252 Processing helix chain 'C' and resid 255 through 268 Processing helix chain 'C' and resid 286 through 301 Processing helix chain 'C' and resid 312 through 316 removed outlier: 3.640A pdb=" N ILE C 315 " --> pdb=" O TYR C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 347 Processing helix chain 'C' and resid 357 through 361 removed outlier: 3.653A pdb=" N TRP C 361 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 375 through 381 removed outlier: 3.957A pdb=" N ALA C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 395 Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 12 through 20 removed outlier: 3.607A pdb=" N LYS D 18 " --> pdb=" O ALA D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 23 No H-bonds generated for 'chain 'D' and resid 21 through 23' Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.502A pdb=" N TYR D 27 " --> pdb=" O ASP D 24 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE D 28 " --> pdb=" O SER D 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 24 through 28' Processing helix chain 'D' and resid 31 through 48 removed outlier: 3.671A pdb=" N PHE D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 62 Processing helix chain 'D' and resid 66 through 80 Processing helix chain 'D' and resid 86 through 118 Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 133 through 143 removed outlier: 3.936A pdb=" N ILE D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 163 Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 204 through 217 Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'D' and resid 245 through 252 Processing helix chain 'D' and resid 255 through 268 Processing helix chain 'D' and resid 286 through 301 Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 327 through 347 Processing helix chain 'D' and resid 357 through 361 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'D' and resid 375 through 380 removed outlier: 4.004A pdb=" N ALA D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 396 Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 12 through 20 removed outlier: 3.594A pdb=" N LYS E 18 " --> pdb=" O ALA E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 28 removed outlier: 3.560A pdb=" N PHE E 28 " --> pdb=" O SER E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 47 Processing helix chain 'E' and resid 52 through 63 Processing helix chain 'E' and resid 66 through 79 Processing helix chain 'E' and resid 86 through 118 Processing helix chain 'E' and resid 130 through 132 No H-bonds generated for 'chain 'E' and resid 130 through 132' Processing helix chain 'E' and resid 133 through 141 removed outlier: 3.534A pdb=" N ALA E 141 " --> pdb=" O ILE E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 166 Processing helix chain 'E' and resid 176 through 184 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 229 through 243 Processing helix chain 'E' and resid 246 through 251 removed outlier: 3.587A pdb=" N ASP E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 269 Processing helix chain 'E' and resid 286 through 301 Processing helix chain 'E' and resid 327 through 347 removed outlier: 3.842A pdb=" N LYS E 333 " --> pdb=" O TYR E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 361 Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 390 through 397 Processing helix chain 'F' and resid 2 through 12 Processing helix chain 'F' and resid 13 through 20 Processing helix chain 'F' and resid 21 through 23 No H-bonds generated for 'chain 'F' and resid 21 through 23' Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 31 through 48 removed outlier: 3.760A pdb=" N ASN F 35 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 62 Processing helix chain 'F' and resid 66 through 80 Processing helix chain 'F' and resid 88 through 118 removed outlier: 3.903A pdb=" N LYS F 92 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 132 No H-bonds generated for 'chain 'F' and resid 130 through 132' Processing helix chain 'F' and resid 133 through 142 removed outlier: 3.660A pdb=" N LEU F 142 " --> pdb=" O MET F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 167 Processing helix chain 'F' and resid 176 through 184 Processing helix chain 'F' and resid 202 through 216 Processing helix chain 'F' and resid 229 through 243 Processing helix chain 'F' and resid 245 through 252 Processing helix chain 'F' and resid 255 through 269 removed outlier: 3.706A pdb=" N LYS F 269 " --> pdb=" O LYS F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 302 Processing helix chain 'F' and resid 327 through 347 Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'H' and resid 4 through 18 removed outlier: 3.547A pdb=" N ASP H 8 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG H 14 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS H 18 " --> pdb=" O ARG H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 82 Processing helix chain 'H' and resid 82 through 96 removed outlier: 3.858A pdb=" N GLU H 88 " --> pdb=" O ASP H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 143 Processing helix chain 'H' and resid 146 through 152 removed outlier: 4.001A pdb=" N LYS H 151 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 167 Processing helix chain 'H' and resid 221 through 225 Processing helix chain 'H' and resid 237 through 242 removed outlier: 3.606A pdb=" N PHE H 241 " --> pdb=" O ASP H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 274 through 287 Processing helix chain 'H' and resid 303 through 312 removed outlier: 3.606A pdb=" N GLY H 312 " --> pdb=" O ILE H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 325 removed outlier: 3.738A pdb=" N ILE H 318 " --> pdb=" O THR H 314 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS H 323 " --> pdb=" O MET H 319 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN H 324 " --> pdb=" O GLU H 320 " (cutoff:3.500A) Processing helix chain 'H' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 153 removed outlier: 6.565A pdb=" N VAL B 221 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LYS B 278 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR B 223 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU B 222 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA B 353 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B 383 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS B 405 " --> pdb=" O MET B 384 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA3, first strand: chain 'A' and resid 427 through 429 removed outlier: 6.511A pdb=" N MET A 384 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU A 192 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N LEU A 385 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 194 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL A 387 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N MET A 196 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N THR A 191 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N THR A 352 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASN A 193 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ALA A 354 " --> pdb=" O ASN A 193 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU A 195 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA A 353 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU A 222 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL A 221 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LYS A 278 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TYR A 223 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 152 through 153 removed outlier: 6.614A pdb=" N VAL C 221 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LYS C 278 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TYR C 223 " --> pdb=" O LYS C 278 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASN C 220 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE C 309 " --> pdb=" O ASN C 220 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU C 222 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA C 353 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE C 383 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N MET C 384 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 172 Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 422 Processing sheet with id=AA7, first strand: chain 'C' and resid 152 through 153 removed outlier: 6.510A pdb=" N VAL D 221 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LYS D 278 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR D 223 " --> pdb=" O LYS D 278 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ILE D 309 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU D 222 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 171 through 172 Processing sheet with id=AA9, first strand: chain 'C' and resid 398 through 399 Processing sheet with id=AB1, first strand: chain 'D' and resid 152 through 153 removed outlier: 3.876A pdb=" N ALA E 353 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA E 354 " --> pdb=" O LEU E 195 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU E 192 " --> pdb=" O PHE E 383 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU E 385 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL E 194 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL E 387 " --> pdb=" O VAL E 194 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N MET E 196 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N MET E 384 " --> pdb=" O ILE E 404 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 171 through 172 Processing sheet with id=AB3, first strand: chain 'D' and resid 349 through 354 removed outlier: 6.037A pdb=" N THR D 191 " --> pdb=" O LEU D 350 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR D 352 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASN D 193 " --> pdb=" O THR D 352 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ALA D 354 " --> pdb=" O ASN D 193 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LEU D 195 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU D 192 " --> pdb=" O PHE D 383 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N LEU D 385 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL D 194 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL D 387 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N MET D 196 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N MET D 384 " --> pdb=" O ILE D 404 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 171 through 172 Processing sheet with id=AB5, first strand: chain 'F' and resid 349 through 352 removed outlier: 3.708A pdb=" N PHE F 383 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 275 through 279 removed outlier: 6.325A pdb=" N LEU F 222 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 419 through 422 Processing sheet with id=AB8, first strand: chain 'H' and resid 23 through 26 Processing sheet with id=AB9, first strand: chain 'H' and resid 124 through 126 removed outlier: 3.753A pdb=" N SER H 193 " --> pdb=" O ILE H 184 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 219 through 220 removed outlier: 3.536A pdb=" N ILE H 248 " --> pdb=" O LEU H 233 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL H 230 " --> pdb=" O VAL H 265 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 290 through 292 removed outlier: 3.508A pdb=" N ALA H 327 " --> pdb=" O VAL H 291 " (cutoff:3.500A) 1158 hydrogen bonds defined for protein. 3303 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.53 Time building geometry restraints manager: 6.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 7549 1.35 - 1.50: 6411 1.50 - 1.65: 10008 1.65 - 1.80: 105 1.80 - 1.95: 124 Bond restraints: 24197 Sorted by residual: bond pdb=" CE1 HIS D 87 " pdb=" NE2 HIS D 87 " ideal model delta sigma weight residual 1.321 1.359 -0.038 1.00e-02 1.00e+04 1.48e+01 bond pdb=" CE1 HIS B 152 " pdb=" NE2 HIS B 152 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.24e+01 bond pdb=" N VAL E 19 " pdb=" CA VAL E 19 " ideal model delta sigma weight residual 1.452 1.492 -0.039 1.18e-02 7.18e+03 1.12e+01 bond pdb=" N TRP D 20 " pdb=" CA TRP D 20 " ideal model delta sigma weight residual 1.462 1.492 -0.030 9.50e-03 1.11e+04 9.92e+00 bond pdb=" N TRP E 20 " pdb=" CA TRP E 20 " ideal model delta sigma weight residual 1.459 1.492 -0.032 1.04e-02 9.25e+03 9.69e+00 ... (remaining 24192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 32329 2.49 - 4.98: 442 4.98 - 7.48: 28 7.48 - 9.97: 7 9.97 - 12.46: 1 Bond angle restraints: 32807 Sorted by residual: angle pdb=" PB AGS C 501 " pdb=" O3B AGS C 501 " pdb=" PG AGS C 501 " ideal model delta sigma weight residual 120.12 132.58 -12.46 3.00e+00 1.11e-01 1.73e+01 angle pdb=" N ASP A 82 " pdb=" CA ASP A 82 " pdb=" C ASP A 82 " ideal model delta sigma weight residual 112.57 108.05 4.52 1.13e+00 7.83e-01 1.60e+01 angle pdb=" N GLU H 92 " pdb=" CA GLU H 92 " pdb=" C GLU H 92 " ideal model delta sigma weight residual 111.71 107.18 4.53 1.15e+00 7.56e-01 1.55e+01 angle pdb=" CA PHE D 383 " pdb=" CB PHE D 383 " pdb=" CG PHE D 383 " ideal model delta sigma weight residual 113.80 117.73 -3.93 1.00e+00 1.00e+00 1.55e+01 angle pdb=" C GLY F 151 " pdb=" N HIS F 152 " pdb=" CA HIS F 152 " ideal model delta sigma weight residual 122.30 117.07 5.23 1.35e+00 5.49e-01 1.50e+01 ... (remaining 32802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 14414 35.65 - 71.31: 202 71.31 - 106.96: 10 106.96 - 142.62: 1 142.62 - 178.27: 4 Dihedral angle restraints: 14631 sinusoidal: 6069 harmonic: 8562 Sorted by residual: dihedral pdb=" O1B AGS E 501 " pdb=" O3B AGS E 501 " pdb=" PB AGS E 501 " pdb=" PG AGS E 501 " ideal model delta sinusoidal sigma weight residual 68.91 -112.82 -178.27 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A AGS F 501 " pdb=" O3A AGS F 501 " pdb=" PA AGS F 501 " pdb=" PB AGS F 501 " ideal model delta sinusoidal sigma weight residual -67.73 106.43 -174.16 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1B AGS B 501 " pdb=" O3B AGS B 501 " pdb=" PB AGS B 501 " pdb=" PG AGS B 501 " ideal model delta sinusoidal sigma weight residual 68.91 -88.62 157.53 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 14628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2650 0.044 - 0.088: 645 0.088 - 0.132: 288 0.132 - 0.176: 48 0.176 - 0.220: 16 Chirality restraints: 3647 Sorted by residual: chirality pdb=" CA ILE H 93 " pdb=" N ILE H 93 " pdb=" C ILE H 93 " pdb=" CB ILE H 93 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA VAL A 150 " pdb=" N VAL A 150 " pdb=" C VAL A 150 " pdb=" CB VAL A 150 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ARG A 124 " pdb=" N ARG A 124 " pdb=" C ARG A 124 " pdb=" CB ARG A 124 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 3644 not shown) Planarity restraints: 4071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 266 " 0.018 2.00e-02 2.50e+03 2.32e-02 1.35e+01 pdb=" CG TRP H 266 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP H 266 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP H 266 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 266 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP H 266 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP H 266 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 266 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 266 " 0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP H 266 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 373 " -0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C GLU A 373 " 0.057 2.00e-02 2.50e+03 pdb=" O GLU A 373 " -0.021 2.00e-02 2.50e+03 pdb=" N SER A 374 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 145 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C SER B 145 " 0.039 2.00e-02 2.50e+03 pdb=" O SER B 145 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE B 146 " -0.013 2.00e-02 2.50e+03 ... (remaining 4068 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 113 2.47 - 3.07: 16357 3.07 - 3.68: 36394 3.68 - 4.29: 55354 4.29 - 4.90: 90583 Nonbonded interactions: 198801 Sorted by model distance: nonbonded pdb=" O1B AGS C 501 " pdb="MG MG C 502 " model vdw 1.856 2.170 nonbonded pdb=" O3B AGS B 501 " pdb="MG MG B 502 " model vdw 1.972 2.170 nonbonded pdb=" OE2 GLU B 227 " pdb="MG MG B 502 " model vdw 1.979 2.170 nonbonded pdb=" O2G AGS E 501 " pdb="MG MG E 502 " model vdw 1.985 2.170 nonbonded pdb=" O2B AGS F 501 " pdb="MG MG F 502 " model vdw 1.993 2.170 ... (remaining 198796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 432) selection = (chain 'C' and resid 1 through 432) selection = (chain 'D' and resid 1 through 432) selection = (chain 'E' and resid 1 through 432) selection = (chain 'F' and resid 1 through 432) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 50.420 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24197 Z= 0.307 Angle : 0.682 12.461 32807 Z= 0.446 Chirality : 0.049 0.220 3647 Planarity : 0.004 0.075 4071 Dihedral : 12.486 178.275 9101 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.78 % Allowed : 7.25 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.16), residues: 2898 helix: 1.29 (0.14), residues: 1435 sheet: -0.35 (0.27), residues: 407 loop : -1.20 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP H 266 HIS 0.008 0.001 HIS B 152 PHE 0.022 0.002 PHE D 383 TYR 0.014 0.001 TYR E 329 ARG 0.004 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.15957 ( 1158) hydrogen bonds : angle 6.57570 ( 3303) covalent geometry : bond 0.00449 (24197) covalent geometry : angle 0.68203 (32807) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 722 time to evaluate : 2.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7054 (m) cc_final: 0.6730 (t) REVERT: A 327 ASN cc_start: 0.3766 (OUTLIER) cc_final: 0.3367 (p0) REVERT: A 347 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7665 (mm-30) REVERT: A 368 MET cc_start: 0.6148 (OUTLIER) cc_final: 0.5816 (ttm) REVERT: A 369 SER cc_start: 0.5907 (m) cc_final: 0.5494 (p) REVERT: B 48 HIS cc_start: 0.7610 (m90) cc_final: 0.7105 (m90) REVERT: B 96 LYS cc_start: 0.8324 (mtpp) cc_final: 0.8100 (mtpp) REVERT: B 267 ARG cc_start: 0.7854 (ttp-170) cc_final: 0.7587 (ttp-170) REVERT: B 422 GLN cc_start: 0.6749 (mt0) cc_final: 0.6413 (mm-40) REVERT: C 128 MET cc_start: 0.5747 (tpp) cc_final: 0.5430 (mmt) REVERT: C 323 VAL cc_start: 0.7577 (t) cc_final: 0.7043 (t) REVERT: D 26 GLU cc_start: 0.7746 (mp0) cc_final: 0.7447 (mm-30) REVERT: D 265 LYS cc_start: 0.7855 (ttmm) cc_final: 0.7465 (tmmt) REVERT: E 109 LYS cc_start: 0.7506 (tptt) cc_final: 0.7221 (ttmt) REVERT: E 338 GLU cc_start: 0.6474 (mt-10) cc_final: 0.6216 (mp0) REVERT: E 380 THR cc_start: 0.8287 (OUTLIER) cc_final: 0.7935 (p) REVERT: F 128 MET cc_start: 0.6055 (ttt) cc_final: 0.5835 (ttm) REVERT: F 156 ASP cc_start: 0.7667 (t0) cc_final: 0.7429 (t0) REVERT: F 167 ASN cc_start: 0.6020 (OUTLIER) cc_final: 0.4854 (m-40) REVERT: F 213 ASP cc_start: 0.7586 (m-30) cc_final: 0.7311 (m-30) REVERT: F 276 ILE cc_start: 0.8836 (mt) cc_final: 0.8628 (tt) REVERT: F 345 GLU cc_start: 0.7727 (tt0) cc_final: 0.7486 (tt0) REVERT: F 355 GLN cc_start: 0.6770 (tt0) cc_final: 0.6483 (pm20) REVERT: F 399 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.6921 (tp40) REVERT: F 423 LYS cc_start: 0.8029 (mttm) cc_final: 0.7779 (mttp) REVERT: H 161 LYS cc_start: 0.4172 (tmmt) cc_final: 0.3865 (mttt) REVERT: H 283 LYS cc_start: 0.7693 (tttt) cc_final: 0.7449 (mtmt) REVERT: H 294 TRP cc_start: 0.7286 (m100) cc_final: 0.7085 (m100) REVERT: H 305 ASN cc_start: 0.6222 (t0) cc_final: 0.5935 (t0) REVERT: H 307 MET cc_start: 0.6672 (mtt) cc_final: 0.6405 (mtt) outliers start: 45 outliers final: 4 residues processed: 750 average time/residue: 0.4087 time to fit residues: 446.6457 Evaluate side-chains 381 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 372 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 10.0000 chunk 220 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 228 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 138 optimal weight: 0.9990 chunk 169 optimal weight: 0.0970 chunk 264 optimal weight: 20.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN A 140 GLN A 167 ASN A 288 ASN A 327 ASN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS C 114 GLN ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN C 288 ASN C 295 ASN D 48 HIS D 116 ASN D 200 ASN E 114 GLN F 8 HIS F 62 ASN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 ASN H 325 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.144749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.117304 restraints weight = 38455.659| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.11 r_work: 0.3327 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24197 Z= 0.131 Angle : 0.553 8.028 32807 Z= 0.301 Chirality : 0.042 0.240 3647 Planarity : 0.004 0.050 4071 Dihedral : 10.802 174.222 3415 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.78 % Allowed : 11.06 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.16), residues: 2898 helix: 1.48 (0.14), residues: 1456 sheet: -0.30 (0.27), residues: 406 loop : -1.15 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 266 HIS 0.014 0.001 HIS B 253 PHE 0.014 0.002 PHE A 417 TYR 0.019 0.001 TYR H 213 ARG 0.007 0.001 ARG B 124 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 1158) hydrogen bonds : angle 5.16870 ( 3303) covalent geometry : bond 0.00281 (24197) covalent geometry : angle 0.55277 (32807) *********************** 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 446 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 401 time to evaluate : 2.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.6624 (tp30) cc_final: 0.6330 (tt0) REVERT: A 118 GLU cc_start: 0.6579 (pp20) cc_final: 0.6329 (pp20) REVERT: A 263 MET cc_start: 0.6972 (mmm) cc_final: 0.6701 (mmm) REVERT: A 302 ASN cc_start: 0.7445 (p0) cc_final: 0.6726 (m-40) REVERT: A 369 SER cc_start: 0.6124 (m) cc_final: 0.5734 (p) REVERT: A 429 VAL cc_start: 0.7887 (m) cc_final: 0.7650 (t) REVERT: B 48 HIS cc_start: 0.7655 (m90) cc_final: 0.7388 (m90) REVERT: B 422 GLN cc_start: 0.6908 (mt0) cc_final: 0.6461 (mm-40) REVERT: C 13 GLN cc_start: 0.7753 (tp40) cc_final: 0.7173 (tp-100) REVERT: C 69 GLU cc_start: 0.7264 (pt0) cc_final: 0.6404 (mm-30) REVERT: C 128 MET cc_start: 0.5951 (tpp) cc_final: 0.5499 (mmt) REVERT: C 158 TYR cc_start: 0.6939 (p90) cc_final: 0.6677 (p90) REVERT: D 26 GLU cc_start: 0.8218 (mp0) cc_final: 0.7816 (mm-30) REVERT: D 247 ASP cc_start: 0.7734 (m-30) cc_final: 0.7447 (t70) REVERT: E 306 THR cc_start: 0.8198 (m) cc_final: 0.7844 (t) REVERT: E 338 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6393 (mp0) REVERT: E 419 MET cc_start: 0.8470 (tpt) cc_final: 0.8185 (tpt) REVERT: F 167 ASN cc_start: 0.5921 (OUTLIER) cc_final: 0.4981 (m-40) REVERT: F 213 ASP cc_start: 0.7539 (m-30) cc_final: 0.7244 (m-30) REVERT: F 226 MET cc_start: 0.8156 (mmm) cc_final: 0.7360 (mmt) REVERT: F 227 GLU cc_start: 0.7101 (pt0) cc_final: 0.6652 (tt0) REVERT: F 355 GLN cc_start: 0.7455 (tt0) cc_final: 0.7017 (pm20) REVERT: F 399 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7091 (tp40) REVERT: H 161 LYS cc_start: 0.4011 (tmmt) cc_final: 0.3607 (mmtt) REVERT: H 260 PHE cc_start: 0.6845 (m-80) cc_final: 0.5671 (m-10) REVERT: H 263 ARG cc_start: 0.5731 (ptt180) cc_final: 0.5126 (mtm110) REVERT: H 292 MET cc_start: 0.7508 (tpp) cc_final: 0.6236 (tpt) REVERT: H 328 GLN cc_start: 0.7444 (pt0) cc_final: 0.7196 (pt0) outliers start: 45 outliers final: 19 residues processed: 434 average time/residue: 0.4052 time to fit residues: 266.8143 Evaluate side-chains 331 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 310 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 0.5980 chunk 5 optimal weight: 8.9990 chunk 199 optimal weight: 20.0000 chunk 116 optimal weight: 7.9990 chunk 280 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 127 optimal weight: 0.0970 chunk 140 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 279 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 140 GLN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN D 13 GLN D 48 HIS D 200 ASN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 252 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.143492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.114795 restraints weight = 38236.477| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.19 r_work: 0.3275 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24197 Z= 0.121 Angle : 0.524 11.676 32807 Z= 0.281 Chirality : 0.041 0.237 3647 Planarity : 0.004 0.049 4071 Dihedral : 10.675 175.377 3407 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.02 % Allowed : 12.33 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.16), residues: 2898 helix: 1.61 (0.14), residues: 1450 sheet: -0.29 (0.27), residues: 407 loop : -1.12 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 20 HIS 0.006 0.001 HIS B 87 PHE 0.022 0.001 PHE C 37 TYR 0.016 0.001 TYR B 329 ARG 0.005 0.000 ARG B 124 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 1158) hydrogen bonds : angle 4.88807 ( 3303) covalent geometry : bond 0.00264 (24197) covalent geometry : angle 0.52445 (32807) *********************** 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 394 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 343 time to evaluate : 2.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.6147 (pp20) cc_final: 0.5835 (pp20) REVERT: A 263 MET cc_start: 0.7031 (mmm) cc_final: 0.6721 (mmm) REVERT: A 330 THR cc_start: 0.7573 (m) cc_final: 0.7337 (t) REVERT: A 380 THR cc_start: 0.7476 (p) cc_final: 0.6956 (t) REVERT: A 389 GLU cc_start: 0.6366 (tp30) cc_final: 0.5810 (tt0) REVERT: B 48 HIS cc_start: 0.7535 (m90) cc_final: 0.7270 (m90) REVERT: B 317 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7581 (pttm) REVERT: B 422 GLN cc_start: 0.6733 (mt0) cc_final: 0.6398 (mm-40) REVERT: C 69 GLU cc_start: 0.7281 (pt0) cc_final: 0.6397 (mm-30) REVERT: C 128 MET cc_start: 0.5795 (tpp) cc_final: 0.5370 (mmt) REVERT: C 188 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7891 (mt-10) REVERT: D 26 GLU cc_start: 0.7941 (mp0) cc_final: 0.7684 (mm-30) REVERT: D 196 MET cc_start: 0.8629 (ptp) cc_final: 0.8419 (ptm) REVERT: E 118 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7464 (tm-30) REVERT: E 306 THR cc_start: 0.8239 (m) cc_final: 0.7872 (t) REVERT: E 338 GLU cc_start: 0.6744 (mt-10) cc_final: 0.6229 (mp0) REVERT: F 167 ASN cc_start: 0.6166 (OUTLIER) cc_final: 0.5063 (m110) REVERT: F 213 ASP cc_start: 0.7317 (m-30) cc_final: 0.7002 (m-30) REVERT: F 399 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7007 (tp40) REVERT: H 34 ARG cc_start: 0.3529 (ttt180) cc_final: 0.2912 (ttm170) REVERT: H 218 LYS cc_start: 0.5432 (mtmt) cc_final: 0.5141 (ttmt) REVERT: H 243 GLU cc_start: 0.7351 (pm20) cc_final: 0.6739 (pm20) REVERT: H 292 MET cc_start: 0.7661 (tpp) cc_final: 0.6255 (tpt) REVERT: H 319 MET cc_start: 0.6174 (mmm) cc_final: 0.4891 (mtm) REVERT: H 328 GLN cc_start: 0.7302 (pt0) cc_final: 0.7034 (pt0) outliers start: 51 outliers final: 31 residues processed: 380 average time/residue: 0.3889 time to fit residues: 226.2379 Evaluate side-chains 341 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 306 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 282 THR Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 207 optimal weight: 6.9990 chunk 247 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 99 optimal weight: 0.4980 chunk 275 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 125 ASN A 140 GLN A 422 GLN B 355 GLN C 35 ASN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN D 114 GLN D 200 ASN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.140688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.111721 restraints weight = 38554.556| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.20 r_work: 0.3221 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24197 Z= 0.150 Angle : 0.538 10.106 32807 Z= 0.289 Chirality : 0.042 0.279 3647 Planarity : 0.004 0.049 4071 Dihedral : 10.740 175.514 3405 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.93 % Allowed : 12.84 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.16), residues: 2898 helix: 1.60 (0.14), residues: 1451 sheet: -0.24 (0.27), residues: 410 loop : -1.17 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 162 HIS 0.006 0.001 HIS B 8 PHE 0.020 0.002 PHE C 37 TYR 0.017 0.001 TYR D 329 ARG 0.004 0.001 ARG B 124 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 1158) hydrogen bonds : angle 4.81586 ( 3303) covalent geometry : bond 0.00345 (24197) covalent geometry : angle 0.53779 (32807) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 334 time to evaluate : 3.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.6176 (pp20) cc_final: 0.5827 (pp20) REVERT: A 263 MET cc_start: 0.7138 (mmm) cc_final: 0.6772 (mmm) REVERT: A 380 THR cc_start: 0.7817 (p) cc_final: 0.7300 (t) REVERT: B 48 HIS cc_start: 0.7624 (m90) cc_final: 0.7349 (m90) REVERT: B 155 MET cc_start: 0.8522 (tpt) cc_final: 0.8295 (tpt) REVERT: B 422 GLN cc_start: 0.6900 (mt0) cc_final: 0.6587 (mm-40) REVERT: C 69 GLU cc_start: 0.7260 (pt0) cc_final: 0.6327 (mm-30) REVERT: C 128 MET cc_start: 0.5758 (tpp) cc_final: 0.5469 (mmt) REVERT: C 138 MET cc_start: 0.7441 (tpt) cc_final: 0.7216 (tpt) REVERT: C 188 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7880 (mt-10) REVERT: D 136 ASP cc_start: 0.7408 (t0) cc_final: 0.7205 (m-30) REVERT: E 24 ASP cc_start: 0.6632 (m-30) cc_final: 0.6417 (m-30) REVERT: E 100 GLN cc_start: 0.8031 (tm-30) cc_final: 0.7759 (tm-30) REVERT: E 118 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7614 (tm-30) REVERT: E 296 GLU cc_start: 0.6190 (mt-10) cc_final: 0.5981 (mt-10) REVERT: E 306 THR cc_start: 0.8294 (m) cc_final: 0.7870 (t) REVERT: E 338 GLU cc_start: 0.6715 (mt-10) cc_final: 0.6134 (mp0) REVERT: E 377 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7897 (mp) REVERT: F 131 VAL cc_start: 0.8183 (OUTLIER) cc_final: 0.7925 (p) REVERT: F 213 ASP cc_start: 0.7325 (m-30) cc_final: 0.7119 (m-30) REVERT: F 367 ASN cc_start: 0.6574 (p0) cc_final: 0.5956 (m-40) REVERT: H 34 ARG cc_start: 0.3599 (ttt180) cc_final: 0.3003 (ttm170) REVERT: H 86 TYR cc_start: 0.5417 (t80) cc_final: 0.5163 (t80) REVERT: H 88 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6263 (mm-30) REVERT: H 292 MET cc_start: 0.7949 (tpp) cc_final: 0.7174 (tpt) REVERT: H 331 MET cc_start: 0.7428 (mmt) cc_final: 0.6975 (mmt) outliers start: 74 outliers final: 49 residues processed: 387 average time/residue: 0.3717 time to fit residues: 223.0710 Evaluate side-chains 353 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 300 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 199 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 202 optimal weight: 0.0970 chunk 92 optimal weight: 0.0570 chunk 104 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 164 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 overall best weight: 1.0098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN D 48 HIS D 114 GLN F 167 ASN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.141699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.112991 restraints weight = 38514.705| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.17 r_work: 0.3249 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 24197 Z= 0.112 Angle : 0.508 9.766 32807 Z= 0.271 Chirality : 0.041 0.249 3647 Planarity : 0.003 0.034 4071 Dihedral : 10.622 174.709 3405 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.94 % Allowed : 14.15 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.16), residues: 2898 helix: 1.71 (0.14), residues: 1453 sheet: -0.12 (0.27), residues: 401 loop : -1.19 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 20 HIS 0.005 0.001 HIS B 8 PHE 0.018 0.001 PHE C 37 TYR 0.013 0.001 TYR C 158 ARG 0.007 0.000 ARG B 124 Details of bonding type rmsd hydrogen bonds : bond 0.03231 ( 1158) hydrogen bonds : angle 4.68681 ( 3303) covalent geometry : bond 0.00243 (24197) covalent geometry : angle 0.50774 (32807) *********************** 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 383 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 334 time to evaluate : 2.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.6186 (pp20) cc_final: 0.5885 (pp20) REVERT: A 263 MET cc_start: 0.7184 (mmm) cc_final: 0.6787 (mmm) REVERT: A 380 THR cc_start: 0.7621 (p) cc_final: 0.7203 (t) REVERT: B 48 HIS cc_start: 0.7564 (m90) cc_final: 0.7330 (m90) REVERT: C 69 GLU cc_start: 0.7286 (pt0) cc_final: 0.6355 (mm-30) REVERT: C 128 MET cc_start: 0.5715 (tpp) cc_final: 0.5412 (mmt) REVERT: C 188 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7883 (mt-10) REVERT: E 23 MET cc_start: 0.8359 (mmt) cc_final: 0.8113 (mmt) REVERT: E 24 ASP cc_start: 0.6616 (m-30) cc_final: 0.6392 (m-30) REVERT: E 77 ILE cc_start: 0.7979 (pt) cc_final: 0.7288 (mt) REVERT: E 100 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7738 (tm-30) REVERT: E 296 GLU cc_start: 0.6104 (mt-10) cc_final: 0.5888 (mt-10) REVERT: E 306 THR cc_start: 0.8222 (m) cc_final: 0.7813 (t) REVERT: E 338 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6087 (mp0) REVERT: E 377 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7896 (mp) REVERT: F 367 ASN cc_start: 0.6701 (p0) cc_final: 0.6105 (m-40) REVERT: F 399 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7157 (tp40) REVERT: H 34 ARG cc_start: 0.3700 (ttt180) cc_final: 0.3112 (ttm170) REVERT: H 86 TYR cc_start: 0.5228 (t80) cc_final: 0.4900 (t80) REVERT: H 88 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.6222 (mm-30) REVERT: H 141 LYS cc_start: 0.5119 (pptt) cc_final: 0.4666 (ttmt) REVERT: H 292 MET cc_start: 0.7950 (tpp) cc_final: 0.6490 (tpt) REVERT: H 303 ASP cc_start: 0.6029 (p0) cc_final: 0.5355 (p0) REVERT: H 307 MET cc_start: 0.6194 (mtm) cc_final: 0.5727 (mpp) outliers start: 49 outliers final: 34 residues processed: 368 average time/residue: 0.3678 time to fit residues: 208.1125 Evaluate side-chains 343 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 306 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 359 GLN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 116 optimal weight: 3.9990 chunk 278 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 192 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 265 optimal weight: 5.9990 chunk 201 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 147 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 403 GLN B 253 HIS ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN D 200 ASN E 114 GLN F 13 GLN ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 ASN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 HIS H 274 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.135604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.107106 restraints weight = 38658.779| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.10 r_work: 0.3161 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 24197 Z= 0.257 Angle : 0.689 10.685 32807 Z= 0.365 Chirality : 0.047 0.253 3647 Planarity : 0.005 0.049 4071 Dihedral : 11.282 178.857 3405 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.25 % Allowed : 13.32 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 2898 helix: 1.15 (0.14), residues: 1445 sheet: -0.20 (0.27), residues: 383 loop : -1.26 (0.18), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 162 HIS 0.007 0.002 HIS B 8 PHE 0.027 0.003 PHE C 37 TYR 0.023 0.002 TYR D 329 ARG 0.007 0.001 ARG F 124 Details of bonding type rmsd hydrogen bonds : bond 0.04308 ( 1158) hydrogen bonds : angle 5.14504 ( 3303) covalent geometry : bond 0.00603 (24197) covalent geometry : angle 0.68864 (32807) *********************** 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 404 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 322 time to evaluate : 2.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.6534 (pp20) cc_final: 0.6155 (pp20) REVERT: C 69 GLU cc_start: 0.7271 (pt0) cc_final: 0.6381 (mm-30) REVERT: C 128 MET cc_start: 0.5880 (tpp) cc_final: 0.5379 (mmt) REVERT: C 188 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8172 (mt-10) REVERT: D 108 SER cc_start: 0.8669 (m) cc_final: 0.8441 (t) REVERT: D 130 ASP cc_start: 0.6560 (t0) cc_final: 0.6081 (m-30) REVERT: E 48 HIS cc_start: 0.6241 (m90) cc_final: 0.5824 (m170) REVERT: E 74 LYS cc_start: 0.7612 (ttmm) cc_final: 0.7397 (ttmm) REVERT: E 77 ILE cc_start: 0.8061 (pt) cc_final: 0.7468 (mt) REVERT: E 124 ARG cc_start: 0.5196 (ptp-170) cc_final: 0.4820 (mtm110) REVERT: E 128 MET cc_start: 0.7333 (mmm) cc_final: 0.7019 (mtp) REVERT: E 269 LYS cc_start: 0.8420 (mttm) cc_final: 0.8021 (mtpt) REVERT: E 377 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8069 (mp) REVERT: F 367 ASN cc_start: 0.6690 (p0) cc_final: 0.6329 (m-40) REVERT: H 49 LYS cc_start: 0.0885 (mttt) cc_final: 0.0671 (ptpt) REVERT: H 88 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.6098 (mm-30) REVERT: H 292 MET cc_start: 0.8419 (tpp) cc_final: 0.8084 (tpp) REVERT: H 303 ASP cc_start: 0.6431 (p0) cc_final: 0.5977 (p0) outliers start: 82 outliers final: 62 residues processed: 386 average time/residue: 0.3801 time to fit residues: 226.6948 Evaluate side-chains 355 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 291 time to evaluate : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 359 GLN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 230 VAL Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 45 optimal weight: 4.9990 chunk 246 optimal weight: 10.0000 chunk 229 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 273 optimal weight: 10.0000 chunk 253 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 HIS ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.137649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.109522 restraints weight = 38791.083| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.10 r_work: 0.3205 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24197 Z= 0.143 Angle : 0.552 10.135 32807 Z= 0.297 Chirality : 0.042 0.222 3647 Planarity : 0.004 0.041 4071 Dihedral : 10.986 178.342 3405 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.58 % Allowed : 14.74 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.16), residues: 2898 helix: 1.42 (0.14), residues: 1446 sheet: -0.08 (0.28), residues: 377 loop : -1.24 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 162 HIS 0.005 0.001 HIS B 8 PHE 0.030 0.002 PHE C 37 TYR 0.025 0.001 TYR D 329 ARG 0.007 0.000 ARG B 124 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 1158) hydrogen bonds : angle 4.84893 ( 3303) covalent geometry : bond 0.00324 (24197) covalent geometry : angle 0.55236 (32807) *********************** 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 380 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 315 time to evaluate : 3.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.6543 (pp20) cc_final: 0.6232 (pp20) REVERT: A 259 TYR cc_start: 0.7566 (t80) cc_final: 0.7019 (t80) REVERT: B 248 ASP cc_start: 0.8322 (m-30) cc_final: 0.8113 (m-30) REVERT: C 69 GLU cc_start: 0.7290 (pt0) cc_final: 0.6418 (mm-30) REVERT: C 128 MET cc_start: 0.5781 (tpp) cc_final: 0.5233 (mmt) REVERT: C 188 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8145 (mt-10) REVERT: D 108 SER cc_start: 0.8594 (m) cc_final: 0.8387 (t) REVERT: E 77 ILE cc_start: 0.8083 (pt) cc_final: 0.7497 (mt) REVERT: E 124 ARG cc_start: 0.5229 (ptp-170) cc_final: 0.4793 (mtm110) REVERT: E 128 MET cc_start: 0.7208 (mmm) cc_final: 0.6916 (mtp) REVERT: E 138 MET cc_start: 0.8372 (mmm) cc_final: 0.8167 (mmm) REVERT: E 269 LYS cc_start: 0.8323 (mttm) cc_final: 0.7883 (mmtm) REVERT: E 338 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6239 (mp0) REVERT: F 367 ASN cc_start: 0.6703 (p0) cc_final: 0.6354 (m-40) REVERT: H 34 ARG cc_start: 0.3849 (ttt180) cc_final: 0.3261 (ttm170) REVERT: H 49 LYS cc_start: 0.1105 (mttt) cc_final: 0.0763 (ptpt) REVERT: H 86 TYR cc_start: 0.5487 (t80) cc_final: 0.5097 (t80) REVERT: H 88 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.6156 (mm-30) REVERT: H 292 MET cc_start: 0.8407 (tpp) cc_final: 0.7641 (tpt) REVERT: H 303 ASP cc_start: 0.6234 (p0) cc_final: 0.5794 (p0) REVERT: H 307 MET cc_start: 0.5994 (OUTLIER) cc_final: 0.5136 (mpp) REVERT: H 309 ARG cc_start: 0.5781 (OUTLIER) cc_final: 0.5456 (ptt180) outliers start: 65 outliers final: 46 residues processed: 366 average time/residue: 0.4346 time to fit residues: 247.0094 Evaluate side-chains 341 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 292 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 359 GLN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 230 VAL Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 307 MET Chi-restraints excluded: chain H residue 309 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 100 optimal weight: 0.0970 chunk 189 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 282 optimal weight: 8.9990 chunk 271 optimal weight: 5.9990 chunk 57 optimal weight: 0.0370 chunk 97 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 ASN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN D 412 ASN ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.139034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110722 restraints weight = 38411.125| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.13 r_work: 0.3233 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24197 Z= 0.111 Angle : 0.531 12.193 32807 Z= 0.282 Chirality : 0.041 0.189 3647 Planarity : 0.003 0.040 4071 Dihedral : 10.784 178.063 3405 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.26 % Allowed : 14.51 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.16), residues: 2898 helix: 1.63 (0.14), residues: 1444 sheet: 0.05 (0.28), residues: 372 loop : -1.27 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 89 HIS 0.004 0.001 HIS B 8 PHE 0.028 0.001 PHE C 104 TYR 0.026 0.001 TYR D 329 ARG 0.007 0.000 ARG B 124 Details of bonding type rmsd hydrogen bonds : bond 0.03166 ( 1158) hydrogen bonds : angle 4.67694 ( 3303) covalent geometry : bond 0.00239 (24197) covalent geometry : angle 0.53052 (32807) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 307 time to evaluate : 2.660 Fit side-chains revert: symmetry clash REVERT: A 259 TYR cc_start: 0.7484 (t80) cc_final: 0.7055 (t80) REVERT: B 48 HIS cc_start: 0.7855 (m90) cc_final: 0.7625 (m90) REVERT: B 158 TYR cc_start: 0.8080 (p90) cc_final: 0.7699 (p90) REVERT: B 200 ASN cc_start: 0.6795 (OUTLIER) cc_final: 0.6569 (m-40) REVERT: B 312 TYR cc_start: 0.7227 (t80) cc_final: 0.6953 (t80) REVERT: C 69 GLU cc_start: 0.7251 (pt0) cc_final: 0.6401 (mm-30) REVERT: C 115 THR cc_start: 0.7474 (m) cc_final: 0.7233 (p) REVERT: C 128 MET cc_start: 0.5673 (tpp) cc_final: 0.5300 (mmt) REVERT: C 188 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8157 (mt-10) REVERT: D 298 LYS cc_start: 0.7303 (ttpt) cc_final: 0.6581 (ptmt) REVERT: E 17 SER cc_start: 0.8277 (t) cc_final: 0.7995 (m) REVERT: E 74 LYS cc_start: 0.7545 (ttmm) cc_final: 0.7341 (ttmm) REVERT: E 77 ILE cc_start: 0.8042 (pt) cc_final: 0.7475 (mt) REVERT: E 112 GLU cc_start: 0.8165 (tt0) cc_final: 0.7902 (tt0) REVERT: E 124 ARG cc_start: 0.5257 (ptp-170) cc_final: 0.4832 (mtm110) REVERT: E 128 MET cc_start: 0.7112 (mmm) cc_final: 0.6862 (mtp) REVERT: E 269 LYS cc_start: 0.8337 (mttm) cc_final: 0.7866 (mmtm) REVERT: E 338 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6383 (mp0) REVERT: F 367 ASN cc_start: 0.6754 (p0) cc_final: 0.6395 (m-40) REVERT: F 399 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7458 (tp40) REVERT: H 34 ARG cc_start: 0.3850 (ttt180) cc_final: 0.3284 (ttm170) REVERT: H 49 LYS cc_start: 0.1260 (mttt) cc_final: 0.0860 (ptpt) REVERT: H 88 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.6168 (mm-30) REVERT: H 292 MET cc_start: 0.8324 (tpp) cc_final: 0.7568 (tpt) REVERT: H 303 ASP cc_start: 0.6225 (p0) cc_final: 0.5816 (p0) REVERT: H 307 MET cc_start: 0.6099 (OUTLIER) cc_final: 0.5212 (mpp) REVERT: H 309 ARG cc_start: 0.5811 (OUTLIER) cc_final: 0.5531 (ptt180) outliers start: 57 outliers final: 46 residues processed: 350 average time/residue: 0.3864 time to fit residues: 208.0588 Evaluate side-chains 335 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 284 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 359 GLN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 230 VAL Chi-restraints excluded: chain H residue 241 PHE Chi-restraints excluded: chain H residue 246 ILE Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 307 MET Chi-restraints excluded: chain H residue 309 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 191 optimal weight: 10.0000 chunk 268 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 243 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 267 optimal weight: 5.9990 chunk 144 optimal weight: 0.0370 overall best weight: 2.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS B 200 ASN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 HIS ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.137604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109336 restraints weight = 38364.445| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.12 r_work: 0.3202 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24197 Z= 0.171 Angle : 0.583 11.573 32807 Z= 0.308 Chirality : 0.043 0.180 3647 Planarity : 0.004 0.042 4071 Dihedral : 10.898 178.330 3405 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.46 % Allowed : 14.98 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.16), residues: 2898 helix: 1.54 (0.14), residues: 1444 sheet: -0.03 (0.28), residues: 378 loop : -1.33 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 162 HIS 0.007 0.001 HIS F 253 PHE 0.026 0.002 PHE C 104 TYR 0.025 0.002 TYR D 329 ARG 0.006 0.001 ARG H 197 Details of bonding type rmsd hydrogen bonds : bond 0.03476 ( 1158) hydrogen bonds : angle 4.79124 ( 3303) covalent geometry : bond 0.00397 (24197) covalent geometry : angle 0.58278 (32807) *********************** 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 344 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 282 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 TYR cc_start: 0.7534 (t80) cc_final: 0.6972 (t80) REVERT: B 48 HIS cc_start: 0.7913 (m90) cc_final: 0.7593 (m90) REVERT: B 158 TYR cc_start: 0.8173 (p90) cc_final: 0.7655 (p90) REVERT: B 312 TYR cc_start: 0.7260 (t80) cc_final: 0.6987 (t80) REVERT: C 69 GLU cc_start: 0.7259 (pt0) cc_final: 0.6384 (mm-30) REVERT: C 115 THR cc_start: 0.7444 (m) cc_final: 0.7210 (p) REVERT: C 128 MET cc_start: 0.5817 (tpp) cc_final: 0.5421 (mmt) REVERT: C 142 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8042 (mt) REVERT: C 188 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8156 (mt-10) REVERT: D 108 SER cc_start: 0.8576 (m) cc_final: 0.8354 (t) REVERT: D 293 LEU cc_start: 0.7626 (tt) cc_final: 0.7253 (tt) REVERT: E 74 LYS cc_start: 0.7575 (ttmm) cc_final: 0.7362 (ttmm) REVERT: E 77 ILE cc_start: 0.8061 (pt) cc_final: 0.7486 (mt) REVERT: E 112 GLU cc_start: 0.8239 (tt0) cc_final: 0.7869 (tt0) REVERT: E 128 MET cc_start: 0.7201 (mmm) cc_final: 0.6998 (mtp) REVERT: E 269 LYS cc_start: 0.8353 (mttm) cc_final: 0.7888 (mmtm) REVERT: E 338 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6441 (mp0) REVERT: F 367 ASN cc_start: 0.6769 (p0) cc_final: 0.6411 (m-40) REVERT: H 49 LYS cc_start: 0.1399 (mttt) cc_final: 0.0807 (ptmt) REVERT: H 88 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6072 (mm-30) REVERT: H 292 MET cc_start: 0.8393 (tpp) cc_final: 0.7962 (tpp) REVERT: H 303 ASP cc_start: 0.6349 (p0) cc_final: 0.5898 (p0) REVERT: H 307 MET cc_start: 0.6104 (OUTLIER) cc_final: 0.5298 (mpp) REVERT: H 309 ARG cc_start: 0.5841 (OUTLIER) cc_final: 0.5531 (ptt180) outliers start: 62 outliers final: 51 residues processed: 330 average time/residue: 0.3648 time to fit residues: 187.5129 Evaluate side-chains 330 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 275 time to evaluate : 2.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 359 GLN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 230 VAL Chi-restraints excluded: chain H residue 246 ILE Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 307 MET Chi-restraints excluded: chain H residue 309 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 221 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 251 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 123 optimal weight: 20.0000 chunk 120 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS B 200 ASN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 HIS ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.139499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.110940 restraints weight = 38525.927| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.15 r_work: 0.3228 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 24197 Z= 0.110 Angle : 0.536 11.907 32807 Z= 0.284 Chirality : 0.041 0.262 3647 Planarity : 0.003 0.041 4071 Dihedral : 10.753 177.843 3405 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.02 % Allowed : 15.42 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.16), residues: 2898 helix: 1.69 (0.14), residues: 1446 sheet: -0.02 (0.28), residues: 382 loop : -1.27 (0.18), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 89 HIS 0.006 0.001 HIS F 253 PHE 0.029 0.001 PHE C 104 TYR 0.026 0.001 TYR D 312 ARG 0.005 0.000 ARG H 197 Details of bonding type rmsd hydrogen bonds : bond 0.03102 ( 1158) hydrogen bonds : angle 4.65047 ( 3303) covalent geometry : bond 0.00239 (24197) covalent geometry : angle 0.53645 (32807) ********************** 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 338 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 287 time to evaluate : 7.493 Fit side-chains revert: symmetry clash REVERT: A 259 TYR cc_start: 0.7536 (t80) cc_final: 0.7099 (t80) REVERT: B 48 HIS cc_start: 0.7886 (m90) cc_final: 0.7670 (m90) REVERT: B 139 ARG cc_start: 0.7720 (ttm-80) cc_final: 0.6811 (mtt-85) REVERT: B 158 TYR cc_start: 0.8092 (p90) cc_final: 0.7683 (p90) REVERT: B 200 ASN cc_start: 0.6799 (OUTLIER) cc_final: 0.6295 (m-40) REVERT: B 312 TYR cc_start: 0.7277 (t80) cc_final: 0.7054 (t80) REVERT: C 69 GLU cc_start: 0.7247 (pt0) cc_final: 0.6369 (mm-30) REVERT: C 115 THR cc_start: 0.7452 (m) cc_final: 0.7228 (p) REVERT: C 128 MET cc_start: 0.5654 (tpp) cc_final: 0.5265 (mmt) REVERT: C 188 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8198 (mt-10) REVERT: D 293 LEU cc_start: 0.7483 (tt) cc_final: 0.7192 (tt) REVERT: D 298 LYS cc_start: 0.7332 (ttpt) cc_final: 0.6641 (ptmt) REVERT: E 74 LYS cc_start: 0.7569 (ttmm) cc_final: 0.7359 (ttmm) REVERT: E 77 ILE cc_start: 0.8011 (pt) cc_final: 0.7505 (mt) REVERT: E 112 GLU cc_start: 0.8239 (tt0) cc_final: 0.7962 (tt0) REVERT: E 269 LYS cc_start: 0.8303 (mttm) cc_final: 0.7839 (mmtm) REVERT: E 338 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6479 (mp0) REVERT: F 367 ASN cc_start: 0.6803 (p0) cc_final: 0.6392 (m-40) REVERT: F 399 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7351 (tp40) REVERT: H 34 ARG cc_start: 0.3856 (ttt180) cc_final: 0.3276 (ttm170) REVERT: H 49 LYS cc_start: 0.1473 (mttt) cc_final: 0.0812 (ptmt) REVERT: H 88 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.6110 (mm-30) REVERT: H 292 MET cc_start: 0.8363 (tpp) cc_final: 0.7923 (tpp) REVERT: H 303 ASP cc_start: 0.6233 (p0) cc_final: 0.6009 (p0) REVERT: H 309 ARG cc_start: 0.5836 (OUTLIER) cc_final: 0.5561 (ptt180) outliers start: 51 outliers final: 41 residues processed: 326 average time/residue: 0.4052 time to fit residues: 210.9249 Evaluate side-chains 324 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 279 time to evaluate : 2.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 359 GLN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 230 VAL Chi-restraints excluded: chain H residue 246 ILE Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 309 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 9 optimal weight: 0.9980 chunk 213 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 193 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 253 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 chunk 274 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS B 200 ASN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 HIS ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.139332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.110363 restraints weight = 38325.926| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.21 r_work: 0.3217 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.179 24197 Z= 0.187 Angle : 0.693 59.189 32807 Z= 0.406 Chirality : 0.046 1.223 3647 Planarity : 0.004 0.125 4071 Dihedral : 10.752 177.852 3405 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.94 % Allowed : 15.66 % Favored : 82.40 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.16), residues: 2898 helix: 1.69 (0.14), residues: 1446 sheet: -0.02 (0.28), residues: 382 loop : -1.28 (0.18), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 89 HIS 0.006 0.001 HIS F 253 PHE 0.027 0.001 PHE C 104 TYR 0.023 0.001 TYR D 329 ARG 0.009 0.000 ARG B 267 Details of bonding type rmsd hydrogen bonds : bond 0.03119 ( 1158) hydrogen bonds : angle 4.65269 ( 3303) covalent geometry : bond 0.00352 (24197) covalent geometry : angle 0.69266 (32807) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14041.47 seconds wall clock time: 246 minutes 49.07 seconds (14809.07 seconds total)