Starting phenix.real_space_refine on Sun Sep 13 13:14:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dw6_27751/09_2026/8dw6_27751.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dw6_27751/09_2026/8dw6_27751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dw6_27751/09_2026/8dw6_27751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dw6_27751/09_2026/8dw6_27751.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dw6_27751/09_2026/8dw6_27751.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dw6_27751/09_2026/8dw6_27751.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dw6_27751/09_2026/8dw6_27751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dw6_27751/09_2026/8dw6_27751.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 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 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23694 Number of models: 1 Model: "" Number of chains: 15 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} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 21079 SG CYS H 37 47.334 75.170 71.878 1.00334.75 S ATOM 21099 SG CYS H 40 46.656 75.858 68.175 1.00325.70 S ATOM 21298 SG CYS H 65 46.615 72.370 69.711 1.00349.75 S ATOM 21324 SG CYS H 68 49.914 74.147 69.241 1.00342.48 S Time building chain proxies: 6.21, per 1000 atoms: 0.26 Number of scatterers: 23694 At special positions: 0 Unit cell: (134.964, 130.824, 141.588, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 132 16.00 P 32 15.00 Mg 5 11.99 O 4586 8.00 N 3943 7.00 C 14995 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 944.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 401 " pdb="ZN ZN H 401 " - pdb=" SG CYS H 65 " pdb="ZN ZN H 401 " - pdb=" SG CYS H 37 " pdb="ZN ZN H 401 " - pdb=" SG CYS H 68 " pdb="ZN ZN H 401 " - pdb=" SG CYS H 40 " Number of angles added : 6 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, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 Processing helix chain 'A' and resid 13 through 20 Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 24 through 28 Processing helix chain 'A' and resid 31 through 47 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 66 through 79 Processing helix chain 'A' and resid 86 through 118 Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 176 through 183 Processing helix chain 'A' and resid 202 through 217 removed outlier: 4.527A pdb=" N GLY A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 243 Processing helix chain 'A' and resid 245 through 252 removed outlier: 3.520A pdb=" N ILE A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 269 removed outlier: 3.551A 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: 3.530A 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: 3.511A 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: 3.569A 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: 3.590A 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: 3.629A 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: 3.639A 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: 3.503A pdb=" N TYR D 27 " --> pdb=" O ASP D 24 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE D 28 " --> pdb=" O SER D 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 24 through 28' Processing helix chain 'D' and resid 31 through 48 Processing helix chain 'D' and resid 52 through 62 Processing helix chain 'D' and resid 66 through 80 Processing helix chain 'D' and resid 86 through 118 Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 133 through 143 removed outlier: 3.936A pdb=" N ILE D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 163 Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 204 through 217 Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'D' and resid 245 through 252 Processing helix chain 'D' and resid 255 through 268 Processing helix chain 'D' and resid 286 through 301 Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 327 through 347 Processing helix chain 'D' and resid 357 through 361 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'D' and resid 375 through 380 removed outlier: 4.004A pdb=" N ALA D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 396 Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 12 through 20 removed outlier: 3.594A 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: 3.586A pdb=" N ASP E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 269 Processing helix chain 'E' and resid 286 through 301 Processing helix chain 'E' and resid 327 through 347 removed outlier: 3.843A pdb=" N LYS E 333 " --> pdb=" O TYR E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 361 Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 390 through 397 Processing helix chain 'F' and resid 2 through 12 Processing helix chain 'F' and resid 13 through 20 Processing helix chain 'F' and resid 21 through 23 No H-bonds generated for 'chain 'F' and resid 21 through 23' Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 31 through 48 removed outlier: 3.759A 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: 3.661A 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 17 Processing helix chain 'H' and resid 74 through 82 Processing helix chain 'H' and resid 82 through 97 removed outlier: 3.694A pdb=" N GLU H 88 " --> pdb=" O ASP H 84 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG H 94 " --> pdb=" O ILE H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 144 Processing helix chain 'H' and resid 147 through 152 Processing helix chain 'H' and resid 158 through 167 Processing helix chain 'H' and resid 221 through 225 Processing helix chain 'H' and resid 235 through 241 removed outlier: 3.805A pdb=" N PHE H 241 " --> pdb=" O ILE H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 274 through 287 Processing helix chain 'H' and resid 303 through 310 Processing helix chain 'H' and resid 314 through 324 Processing helix chain 'H' and resid 329 through 340 removed outlier: 3.549A pdb=" N LYS H 338 " --> pdb=" O MET H 334 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 153 removed outlier: 6.564A pdb=" N VAL B 221 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LYS B 278 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR B 223 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU B 222 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA B 353 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.626A 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: 6.512A 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: 7.742A pdb=" N THR A 352 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASN A 193 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ALA A 354 " --> pdb=" O ASN A 193 " (cutoff:3.500A) removed outlier: 5.955A 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: 7.739A pdb=" N LYS A 278 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TYR A 223 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 152 through 153 removed outlier: 6.615A pdb=" N VAL C 221 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LYS C 278 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.243A 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: 7.639A pdb=" N ILE C 309 " --> pdb=" O ASN C 220 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU C 222 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA C 353 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE C 383 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N MET C 384 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 172 Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 422 Processing sheet with id=AA7, first strand: chain 'C' and resid 152 through 153 removed outlier: 6.511A pdb=" N VAL D 221 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 7.747A 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: 7.490A 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: 6.324A pdb=" N VAL E 194 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL E 387 " --> pdb=" O VAL E 194 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N MET E 196 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N MET E 384 " --> pdb=" O ILE E 404 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 171 through 172 Processing sheet with id=AB3, first strand: chain 'D' and resid 349 through 354 removed outlier: 6.037A pdb=" N THR D 191 " --> pdb=" O LEU D 350 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR D 352 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN D 193 " --> pdb=" O THR D 352 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ALA D 354 " --> pdb=" O ASN D 193 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LEU D 195 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 6.391A 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: 7.511A pdb=" N VAL D 387 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 6.489A 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: 6.324A pdb=" N LEU F 222 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 419 through 422 Processing sheet with id=AB8, first strand: chain 'H' and resid 32 through 35 Processing sheet with id=AB9, first strand: chain 'H' and resid 124 through 126 removed outlier: 5.826A pdb=" N LEU H 180 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY H 196 " --> pdb=" O LEU H 180 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE H 182 " --> pdb=" O PHE H 194 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE H 194 " --> pdb=" O ILE H 182 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE H 184 " --> pdb=" O GLU H 192 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 219 through 220 removed outlier: 4.026A pdb=" N ILE H 248 " --> pdb=" O LEU H 233 " (cutoff:3.500A) removed outlier: 6.062A 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 1155 hydrogen bonds defined for protein. 3303 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.45 Time building geometry restraints manager: 2.79 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: 7554 1.35 - 1.50: 6439 1.50 - 1.65: 9975 1.65 - 1.80: 113 1.80 - 1.95: 116 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 1.360 -0.039 1.00e-02 1.00e+04 1.54e+01 bond pdb=" CE1 HIS B 152 " pdb=" NE2 HIS B 152 " ideal model delta sigma weight residual 1.321 1.357 -0.036 1.00e-02 1.00e+04 1.27e+01 bond pdb=" N VAL E 19 " pdb=" CA VAL E 19 " ideal model delta sigma weight residual 1.452 1.492 -0.039 1.18e-02 7.18e+03 1.12e+01 bond pdb=" C3' DT M 16 " pdb=" C2' DT M 16 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" N TRP E 20 " pdb=" CA TRP E 20 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.04e-02 9.25e+03 1.02e+01 ... (remaining 24192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 32367 2.49 - 4.99: 415 4.99 - 7.48: 20 7.48 - 9.97: 4 9.97 - 12.46: 1 Bond angle restraints: 32807 Sorted by residual: angle pdb=" O SER B 63 " pdb=" C SER B 63 " pdb=" N SER B 64 " ideal model delta sigma weight residual 120.83 124.40 -3.57 7.40e-01 1.83e+00 2.32e+01 angle pdb=" N3 DT M 15 " pdb=" C4 DT M 15 " pdb=" O4 DT M 15 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT M 9 " pdb=" C4 DT M 9 " pdb=" O4 DT M 9 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" PB AGS C 501 " pdb=" O3B AGS C 501 " pdb=" PG AGS C 501 " ideal model delta sigma weight residual 120.12 132.58 -12.46 3.00e+00 1.11e-01 1.73e+01 angle pdb=" N3 DT M 11 " pdb=" C4 DT M 11 " pdb=" O4 DT M 11 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 ... (remaining 32802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 14390 35.65 - 71.31: 175 71.31 - 106.96: 6 106.96 - 142.62: 1 142.62 - 178.27: 4 Dihedral angle restraints: 14576 sinusoidal: 6014 harmonic: 8562 Sorted by residual: dihedral pdb=" O1B AGS E 501 " pdb=" O3B AGS E 501 " pdb=" PB AGS E 501 " pdb=" PG AGS E 501 " ideal model delta sinusoidal sigma weight residual 68.91 -112.82 -178.27 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A AGS F 501 " pdb=" O3A AGS F 501 " pdb=" PA AGS F 501 " pdb=" PB AGS F 501 " ideal model delta sinusoidal sigma weight residual -67.73 106.44 -174.17 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1B AGS B 501 " pdb=" O3B AGS B 501 " pdb=" PB AGS B 501 " pdb=" PG AGS B 501 " ideal model delta sinusoidal sigma weight residual 68.91 -88.60 157.51 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 14573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2656 0.043 - 0.087: 656 0.087 - 0.130: 289 0.130 - 0.173: 32 0.173 - 0.217: 14 Chirality restraints: 3647 Sorted by residual: 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 1.17e+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 1.16e+00 chirality pdb=" CA VAL D 310 " pdb=" N VAL D 310 " pdb=" C VAL D 310 " pdb=" CB VAL D 310 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 3644 not shown) Planarity restraints: 4071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 373 " -0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C GLU A 373 " 0.058 2.00e-02 2.50e+03 pdb=" O GLU A 373 " -0.021 2.00e-02 2.50e+03 pdb=" N SER A 374 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 145 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.11e+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 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 402 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.39e+00 pdb=" C LYS A 402 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS A 402 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN A 403 " 0.012 2.00e-02 2.50e+03 ... (remaining 4068 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.46: 130 2.46 - 3.07: 16732 3.07 - 3.68: 36697 3.68 - 4.29: 55693 4.29 - 4.90: 91037 Nonbonded interactions: 200289 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 200284 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.320 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: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 25.860 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 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 0.049 24201 Z= 0.308 Angle : 0.657 12.463 32813 Z= 0.444 Chirality : 0.047 0.217 3647 Planarity : 0.004 0.075 4071 Dihedral : 12.021 178.273 9046 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.26 % Allowed : 6.70 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.16), residues: 2898 helix: 1.44 (0.14), residues: 1431 sheet: -0.28 (0.28), residues: 391 loop : -1.00 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 143 TYR 0.014 0.001 TYR E 329 PHE 0.022 0.002 PHE D 383 TRP 0.027 0.001 TRP F 351 HIS 0.008 0.001 HIS B 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.31 (24197) covalent geometry : angle 0.65606 / 0.44 (32807) hydrogen bonds : bond 0.15726 / 11.07 ( 1155) hydrogen bonds : angle 6.43487 / 4.60 ( 3303) metal coordination : bond 0.01309 / 0.66 ( 4) metal coordination : angle 3.14693 / 1.60 ( 6) *********************** 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 859 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 802 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 PHE cc_start: 0.6112 (m-80) cc_final: 0.5698 (m-80) REVERT: A 12 ASP cc_start: 0.6533 (t0) cc_final: 0.5714 (m-30) REVERT: A 100 GLN cc_start: 0.7097 (mt0) cc_final: 0.6572 (tm-30) REVERT: A 121 PRO cc_start: 0.5631 (Cg_exo) cc_final: 0.5398 (Cg_endo) REVERT: A 196 MET cc_start: 0.6497 (mmt) cc_final: 0.5187 (ptm) REVERT: A 291 ARG cc_start: 0.5841 (mtm-85) cc_final: 0.5410 (mtt180) REVERT: A 337 GLU cc_start: 0.5584 (mt-10) cc_final: 0.5094 (mt-10) REVERT: A 418 LEU cc_start: 0.5957 (mp) cc_final: 0.5704 (mt) REVERT: B 7 SER cc_start: 0.8367 (m) cc_final: 0.8118 (p) REVERT: B 41 LYS cc_start: 0.7079 (ttpt) cc_final: 0.6740 (tttt) REVERT: B 188 GLU cc_start: 0.6146 (mt-10) cc_final: 0.5848 (mt-10) REVERT: B 196 MET cc_start: 0.4982 (mtm) cc_final: 0.4437 (mtp) REVERT: B 228 MET cc_start: 0.5909 (mtm) cc_final: 0.5294 (mtp) REVERT: B 288 ASN cc_start: 0.6941 (m-40) cc_final: 0.6732 (m110) REVERT: B 296 GLU cc_start: 0.5907 (tt0) cc_final: 0.5567 (tt0) REVERT: B 320 ARG cc_start: 0.5952 (mtm180) cc_final: 0.5725 (mtm-85) REVERT: B 384 MET cc_start: 0.7524 (mtt) cc_final: 0.7208 (mtp) REVERT: C 19 VAL cc_start: 0.8440 (OUTLIER) cc_final: 0.8205 (m) REVERT: C 39 LEU cc_start: 0.8084 (mt) cc_final: 0.7819 (mp) REVERT: C 47 TYR cc_start: 0.4941 (m-80) cc_final: 0.4543 (m-80) REVERT: C 168 LYS cc_start: 0.6696 (mptt) cc_final: 0.6371 (mmmt) REVERT: C 228 MET cc_start: 0.6258 (mtm) cc_final: 0.5873 (mtt) REVERT: C 295 ASN cc_start: 0.7874 (t0) cc_final: 0.7668 (t0) REVERT: D 1 MET cc_start: 0.6411 (ptm) cc_final: 0.5957 (ptm) REVERT: D 3 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6465 (tt0) REVERT: D 41 LYS cc_start: 0.6231 (ttpp) cc_final: 0.5668 (pttp) REVERT: D 128 MET cc_start: 0.6819 (tpp) cc_final: 0.6266 (ttm) REVERT: D 155 MET cc_start: 0.6181 (tpt) cc_final: 0.5956 (tpt) REVERT: D 166 MET cc_start: 0.3289 (pmm) cc_final: 0.3035 (mtp) REVERT: D 244 VAL cc_start: 0.7519 (p) cc_final: 0.7303 (t) REVERT: D 303 PHE cc_start: 0.6660 (t80) cc_final: 0.6224 (t80) REVERT: D 304 VAL cc_start: 0.6499 (t) cc_final: 0.6292 (p) REVERT: D 398 GLN cc_start: 0.5966 (mt0) cc_final: 0.5601 (pt0) REVERT: E 16 PHE cc_start: 0.6732 (t80) cc_final: 0.6512 (t80) REVERT: E 32 PRO cc_start: 0.5070 (Cg_endo) cc_final: 0.4827 (Cg_exo) REVERT: E 43 HIS cc_start: 0.4527 (t-90) cc_final: 0.4190 (t70) REVERT: E 115 THR cc_start: 0.7155 (m) cc_final: 0.6918 (t) REVERT: E 116 ASN cc_start: 0.6361 (t0) cc_final: 0.6003 (t0) REVERT: E 243 ASP cc_start: 0.6967 (t0) cc_final: 0.6739 (t0) REVERT: E 312 TYR cc_start: 0.1230 (t80) cc_final: 0.1009 (t80) REVERT: E 380 THR cc_start: 0.4910 (OUTLIER) cc_final: 0.4622 (m) REVERT: E 427 LYS cc_start: 0.6165 (ttpp) cc_final: 0.5812 (ptmt) REVERT: F 11 PHE cc_start: 0.7538 (m-80) cc_final: 0.6708 (m-80) REVERT: F 75 THR cc_start: 0.6246 (m) cc_final: 0.5802 (t) REVERT: F 139 ARG cc_start: 0.5517 (ttm-80) cc_final: 0.5103 (mtt-85) REVERT: F 274 ARG cc_start: 0.4448 (mtm-85) cc_final: 0.4054 (mtt90) REVERT: F 370 ASP cc_start: 0.4897 (m-30) cc_final: 0.4599 (m-30) REVERT: F 384 MET cc_start: 0.6003 (mtp) cc_final: 0.5500 (ttm) REVERT: F 423 LYS cc_start: 0.6348 (mttm) cc_final: 0.5188 (pttm) REVERT: H 18 HIS cc_start: 0.3467 (OUTLIER) cc_final: 0.3030 (p-80) REVERT: H 86 TYR cc_start: 0.4931 (t80) cc_final: 0.4637 (t80) REVERT: H 143 ARG cc_start: 0.4873 (mmt180) cc_final: 0.4622 (tpp80) REVERT: H 145 ILE cc_start: 0.5506 (mm) cc_final: 0.5258 (mm) REVERT: H 180 LEU cc_start: 0.6327 (mt) cc_final: 0.6063 (mt) REVERT: H 276 ASP cc_start: 0.6957 (OUTLIER) cc_final: 0.6337 (m-30) REVERT: H 279 LYS cc_start: 0.7912 (tttt) cc_final: 0.7692 (ptmt) REVERT: H 299 TRP cc_start: 0.7266 (m-90) cc_final: 0.6909 (m-90) outliers start: 57 outliers final: 7 residues processed: 839 average time/residue: 0.1933 time to fit residues: 243.6121 Evaluate side-chains 430 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 419 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 276 ASP Chi-restraints excluded: chain H residue 282 THR Chi-restraints excluded: chain H residue 295 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 HIS A 116 ASN A 167 ASN A 253 HIS A 302 ASN A 327 ASN A 425 ASN B 8 HIS B 100 GLN B 403 GLN C 114 GLN C 140 GLN D 35 ASN D 57 ASN D 99 GLN D 116 ASN D 422 GLN E 87 HIS E 403 GLN E 412 ASN F 62 ASN F 302 ASN F 403 GLN H 317 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.154832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.132140 restraints weight = 43558.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.132260 restraints weight = 30831.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.133207 restraints weight = 24305.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.133966 restraints weight = 20843.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.134114 restraints weight = 18244.206| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.155 24201 Z= 0.251 Angle : 0.751 10.687 32813 Z= 0.404 Chirality : 0.049 0.364 3647 Planarity : 0.006 0.067 4071 Dihedral : 10.421 170.989 3359 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.89 % Allowed : 12.37 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.15), residues: 2898 helix: 0.82 (0.14), residues: 1462 sheet: -0.45 (0.26), residues: 400 loop : -1.17 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 161 TYR 0.029 0.003 TYR F 312 PHE 0.027 0.003 PHE F 383 TRP 0.035 0.003 TRP F 428 HIS 0.008 0.002 HIS F 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.25 (24197) covalent geometry : angle 0.74691 / 0.40 (32807) hydrogen bonds : bond 0.04859 / 3.26 ( 1155) hydrogen bonds : angle 5.34271 / 3.84 ( 3303) metal coordination : bond 0.01021 / 0.53 ( 4) metal coordination : angle 5.74973 / 3.03 ( 6) *********************** 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 538 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 465 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.6538 (t0) cc_final: 0.5714 (m-30) REVERT: A 100 GLN cc_start: 0.6849 (mt0) cc_final: 0.6553 (tm-30) REVERT: A 121 PRO cc_start: 0.5666 (Cg_exo) cc_final: 0.5464 (Cg_endo) REVERT: A 385 LEU cc_start: 0.6598 (mt) cc_final: 0.6237 (tp) REVERT: A 418 LEU cc_start: 0.5873 (mp) cc_final: 0.4957 (mp) REVERT: A 425 ASN cc_start: 0.4364 (t160) cc_final: 0.4106 (t0) REVERT: B 128 MET cc_start: 0.3661 (ttt) cc_final: 0.3259 (ttm) REVERT: B 418 LEU cc_start: 0.6574 (tp) cc_final: 0.6052 (tt) REVERT: C 39 LEU cc_start: 0.7852 (mt) cc_final: 0.7642 (mt) REVERT: C 112 GLU cc_start: 0.6580 (tt0) cc_final: 0.6360 (tt0) REVERT: C 295 ASN cc_start: 0.7376 (t0) cc_final: 0.7146 (t0) REVERT: D 1 MET cc_start: 0.6346 (ptm) cc_final: 0.5852 (ptm) REVERT: D 3 GLU cc_start: 0.6788 (mt-10) cc_final: 0.6473 (tt0) REVERT: D 41 LYS cc_start: 0.6448 (ttpp) cc_final: 0.5863 (pttp) REVERT: D 128 MET cc_start: 0.6908 (tpp) cc_final: 0.6257 (ttm) REVERT: D 153 ASP cc_start: 0.6103 (t0) cc_final: 0.5819 (t0) REVERT: D 251 ASP cc_start: 0.6514 (m-30) cc_final: 0.6266 (m-30) REVERT: D 303 PHE cc_start: 0.6645 (t80) cc_final: 0.6350 (t80) REVERT: D 363 SER cc_start: 0.4491 (p) cc_final: 0.4234 (t) REVERT: E 32 PRO cc_start: 0.5251 (Cg_endo) cc_final: 0.5005 (Cg_exo) REVERT: E 43 HIS cc_start: 0.4656 (t-90) cc_final: 0.4184 (t-170) REVERT: E 76 LEU cc_start: 0.5829 (OUTLIER) cc_final: 0.5266 (mt) REVERT: E 115 THR cc_start: 0.6757 (m) cc_final: 0.6535 (t) REVERT: E 124 ARG cc_start: 0.4454 (OUTLIER) cc_final: 0.3860 (ptm-80) REVERT: E 427 LYS cc_start: 0.6153 (ttpp) cc_final: 0.5769 (ptmt) REVERT: F 9 LEU cc_start: 0.5960 (mt) cc_final: 0.5757 (mt) REVERT: F 120 PRO cc_start: 0.4146 (Cg_endo) cc_final: 0.3934 (Cg_exo) REVERT: F 248 ASP cc_start: 0.4981 (m-30) cc_final: 0.4547 (m-30) REVERT: F 263 MET cc_start: 0.6570 (mmm) cc_final: 0.5841 (tmm) REVERT: F 265 LYS cc_start: 0.7008 (mmtm) cc_final: 0.6562 (mtmm) REVERT: F 274 ARG cc_start: 0.4579 (mtm-85) cc_final: 0.3997 (mtt90) REVERT: F 298 LYS cc_start: 0.6523 (mtmt) cc_final: 0.5943 (mppt) REVERT: F 384 MET cc_start: 0.5939 (mtp) cc_final: 0.5452 (ttm) REVERT: F 423 LYS cc_start: 0.6283 (mttm) cc_final: 0.5049 (pttm) REVERT: H 51 ARG cc_start: 0.4390 (mtt180) cc_final: 0.4069 (mtp180) REVERT: H 92 GLU cc_start: 0.5328 (tp30) cc_final: 0.4810 (tp30) REVERT: H 154 TRP cc_start: 0.3111 (m-90) cc_final: 0.2679 (m-90) REVERT: H 193 SER cc_start: 0.4888 (m) cc_final: 0.4461 (m) REVERT: H 278 ILE cc_start: 0.8067 (pp) cc_final: 0.7797 (mm) REVERT: H 303 ASP cc_start: 0.5131 (p0) cc_final: 0.4243 (p0) REVERT: H 305 ASN cc_start: 0.6775 (t0) cc_final: 0.6359 (p0) REVERT: H 308 ILE cc_start: 0.7855 (mt) cc_final: 0.7498 (pt) REVERT: H 311 GLU cc_start: 0.5098 (OUTLIER) cc_final: 0.4788 (mm-30) outliers start: 73 outliers final: 38 residues processed: 518 average time/residue: 0.1761 time to fit residues: 141.1893 Evaluate side-chains 403 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 362 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain H residue 148 ASP Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 311 GLU Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 248 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 178 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN B 100 GLN B 216 GLN C 57 ASN C 100 GLN C 367 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN D 99 GLN D 253 HIS E 87 HIS F 8 HIS F 398 GLN ** H 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.154831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.132741 restraints weight = 43261.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.131979 restraints weight = 33055.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.133249 restraints weight = 26743.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.134560 restraints weight = 21932.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.134449 restraints weight = 19531.711| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24201 Z= 0.154 Angle : 0.613 9.127 32813 Z= 0.326 Chirality : 0.044 0.278 3647 Planarity : 0.004 0.059 4071 Dihedral : 10.241 168.245 3347 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.69 % Allowed : 13.44 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.16), residues: 2898 helix: 0.94 (0.14), residues: 1460 sheet: -0.41 (0.27), residues: 386 loop : -1.22 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 179 TYR 0.032 0.002 TYR D 165 PHE 0.023 0.002 PHE H 194 TRP 0.044 0.002 TRP F 428 HIS 0.004 0.001 HIS F 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (24197) covalent geometry : angle 0.61023 / 0.33 (32807) hydrogen bonds : bond 0.04105 / 2.76 ( 1155) hydrogen bonds : angle 5.05671 / 3.66 ( 3303) metal coordination : bond 0.00561 / 0.28 ( 4) metal coordination : angle 4.14412 / 2.08 ( 6) *********************** 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 490 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 397 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.6342 (t0) cc_final: 0.5632 (m-30) REVERT: A 100 GLN cc_start: 0.6917 (mt0) cc_final: 0.6586 (tm-30) REVERT: A 121 PRO cc_start: 0.5807 (Cg_exo) cc_final: 0.5602 (Cg_endo) REVERT: A 385 LEU cc_start: 0.6581 (mt) cc_final: 0.6221 (tp) REVERT: A 425 ASN cc_start: 0.3716 (t160) cc_final: 0.3479 (t0) REVERT: B 296 GLU cc_start: 0.5876 (tt0) cc_final: 0.5531 (tt0) REVERT: B 418 LEU cc_start: 0.6615 (tp) cc_final: 0.6065 (tt) REVERT: C 39 LEU cc_start: 0.7810 (mt) cc_final: 0.7607 (mt) REVERT: C 155 MET cc_start: 0.6843 (tpp) cc_final: 0.6455 (tpp) REVERT: D 1 MET cc_start: 0.6362 (ptm) cc_final: 0.5857 (ptm) REVERT: D 3 GLU cc_start: 0.6770 (mt-10) cc_final: 0.6318 (tt0) REVERT: D 23 MET cc_start: 0.7535 (mmt) cc_final: 0.7281 (mmp) REVERT: D 24 ASP cc_start: 0.6758 (OUTLIER) cc_final: 0.6397 (m-30) REVERT: D 41 LYS cc_start: 0.6441 (ttpp) cc_final: 0.5829 (pttp) REVERT: D 128 MET cc_start: 0.6802 (tpp) cc_final: 0.6201 (ttm) REVERT: D 303 PHE cc_start: 0.6702 (t80) cc_final: 0.6435 (t80) REVERT: D 344 VAL cc_start: 0.6885 (m) cc_final: 0.6612 (t) REVERT: D 363 SER cc_start: 0.4348 (p) cc_final: 0.4087 (t) REVERT: E 32 PRO cc_start: 0.5045 (Cg_endo) cc_final: 0.4810 (Cg_exo) REVERT: E 76 LEU cc_start: 0.5913 (OUTLIER) cc_final: 0.5489 (mt) REVERT: E 377 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.5859 (mt) REVERT: E 427 LYS cc_start: 0.6215 (ttpp) cc_final: 0.5868 (ptmt) REVERT: F 9 LEU cc_start: 0.5961 (mt) cc_final: 0.5636 (mt) REVERT: F 75 THR cc_start: 0.6344 (p) cc_final: 0.6108 (t) REVERT: F 79 LYS cc_start: 0.6665 (mttm) cc_final: 0.6212 (ttmm) REVERT: F 201 VAL cc_start: 0.5578 (OUTLIER) cc_final: 0.5322 (t) REVERT: F 263 MET cc_start: 0.6523 (mmm) cc_final: 0.5768 (tmm) REVERT: F 265 LYS cc_start: 0.7018 (mmtm) cc_final: 0.6510 (mmtp) REVERT: F 274 ARG cc_start: 0.4632 (mtm-85) cc_final: 0.4075 (mtt90) REVERT: F 298 LYS cc_start: 0.6406 (mtmt) cc_final: 0.5881 (mppt) REVERT: F 384 MET cc_start: 0.5511 (mtp) cc_final: 0.5035 (ttm) REVERT: F 423 LYS cc_start: 0.6389 (mttm) cc_final: 0.4660 (ptmm) REVERT: H 94 ARG cc_start: 0.5679 (OUTLIER) cc_final: 0.5022 (ttm110) REVERT: H 154 TRP cc_start: 0.3070 (m-90) cc_final: 0.2674 (m-90) REVERT: H 193 SER cc_start: 0.4960 (m) cc_final: 0.4616 (m) REVERT: H 242 ILE cc_start: 0.5300 (mm) cc_final: 0.4960 (mm) REVERT: H 255 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.5946 (mp) REVERT: H 278 ILE cc_start: 0.8024 (pp) cc_final: 0.7790 (mm) REVERT: H 294 TRP cc_start: 0.7054 (m100) cc_final: 0.6639 (m100) REVERT: H 303 ASP cc_start: 0.5075 (p0) cc_final: 0.4406 (p0) REVERT: H 308 ILE cc_start: 0.7842 (mt) cc_final: 0.7558 (pt) outliers start: 93 outliers final: 45 residues processed: 468 average time/residue: 0.1701 time to fit residues: 125.1795 Evaluate side-chains 382 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 331 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain H residue 148 ASP Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 299 TRP Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 236 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 chunk 268 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 289 optimal weight: 8.9990 chunk 288 optimal weight: 4.9990 chunk 128 optimal weight: 9.9990 chunk 285 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN B 200 ASN B 399 GLN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS E 87 HIS ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 ASN ** 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 = 0.4147 r_free = 0.4147 target = 0.153345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.129993 restraints weight = 43433.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.130957 restraints weight = 32139.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.132113 restraints weight = 24069.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.132547 restraints weight = 19035.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.132812 restraints weight = 17556.437| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24201 Z= 0.167 Angle : 0.614 7.932 32813 Z= 0.327 Chirality : 0.044 0.306 3647 Planarity : 0.004 0.045 4071 Dihedral : 10.317 165.100 3347 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.92 % Allowed : 13.71 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.16), residues: 2898 helix: 0.91 (0.14), residues: 1458 sheet: -0.44 (0.27), residues: 395 loop : -1.36 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 322 TYR 0.023 0.002 TYR D 15 PHE 0.020 0.002 PHE A 28 TRP 0.052 0.002 TRP F 428 HIS 0.010 0.002 HIS E 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (24197) covalent geometry : angle 0.61045 / 0.33 (32807) hydrogen bonds : bond 0.03998 / 2.67 ( 1155) hydrogen bonds : angle 4.99177 / 3.60 ( 3303) metal coordination : bond 0.00621 / 0.31 ( 4) metal coordination : angle 4.79905 / 2.48 ( 6) *********************** 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 461 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 362 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.6367 (t0) cc_final: 0.5687 (m-30) REVERT: A 100 GLN cc_start: 0.6937 (mt0) cc_final: 0.6616 (tm-30) REVERT: A 385 LEU cc_start: 0.6580 (mt) cc_final: 0.6230 (tp) REVERT: B 56 LEU cc_start: 0.7731 (mt) cc_final: 0.7489 (tp) REVERT: B 296 GLU cc_start: 0.5850 (tt0) cc_final: 0.5519 (tt0) REVERT: B 418 LEU cc_start: 0.6611 (tp) cc_final: 0.6074 (tt) REVERT: D 1 MET cc_start: 0.6331 (ptm) cc_final: 0.5819 (ptm) REVERT: D 3 GLU cc_start: 0.6771 (mt-10) cc_final: 0.6351 (tt0) REVERT: D 24 ASP cc_start: 0.6690 (OUTLIER) cc_final: 0.6390 (m-30) REVERT: D 41 LYS cc_start: 0.6531 (ttpp) cc_final: 0.5936 (pttp) REVERT: D 128 MET cc_start: 0.6887 (tpp) cc_final: 0.6316 (ttm) REVERT: D 303 PHE cc_start: 0.6765 (t80) cc_final: 0.6516 (t80) REVERT: D 363 SER cc_start: 0.4825 (p) cc_final: 0.4605 (t) REVERT: E 32 PRO cc_start: 0.5056 (Cg_endo) cc_final: 0.4840 (Cg_exo) REVERT: E 43 HIS cc_start: 0.3922 (t70) cc_final: 0.3530 (t70) REVERT: E 76 LEU cc_start: 0.5923 (OUTLIER) cc_final: 0.5499 (mt) REVERT: E 124 ARG cc_start: 0.4470 (OUTLIER) cc_final: 0.4062 (ptm160) REVERT: E 131 VAL cc_start: 0.7175 (m) cc_final: 0.6876 (p) REVERT: E 377 LEU cc_start: 0.6637 (OUTLIER) cc_final: 0.5941 (mt) REVERT: E 427 LYS cc_start: 0.6352 (ttpp) cc_final: 0.6045 (ptmt) REVERT: F 9 LEU cc_start: 0.5895 (mt) cc_final: 0.5469 (mt) REVERT: F 201 VAL cc_start: 0.5445 (OUTLIER) cc_final: 0.5148 (t) REVERT: F 263 MET cc_start: 0.6246 (mmm) cc_final: 0.5765 (tmm) REVERT: F 265 LYS cc_start: 0.7047 (mmtm) cc_final: 0.6527 (mmtp) REVERT: F 274 ARG cc_start: 0.4501 (mtm-85) cc_final: 0.3919 (mtt90) REVERT: F 384 MET cc_start: 0.5726 (mtp) cc_final: 0.5309 (ttm) REVERT: F 423 LYS cc_start: 0.6275 (mttm) cc_final: 0.4513 (ptmm) REVERT: H 94 ARG cc_start: 0.5593 (OUTLIER) cc_final: 0.5014 (ttm110) REVERT: H 154 TRP cc_start: 0.3065 (m-90) cc_final: 0.2654 (m-90) REVERT: H 220 TYR cc_start: 0.5824 (t80) cc_final: 0.5359 (t80) REVERT: H 242 ILE cc_start: 0.5464 (mm) cc_final: 0.5112 (mm) REVERT: H 255 LEU cc_start: 0.6257 (OUTLIER) cc_final: 0.5975 (mp) REVERT: H 294 TRP cc_start: 0.7094 (m100) cc_final: 0.6725 (m100) REVERT: H 305 ASN cc_start: 0.6124 (p0) cc_final: 0.5869 (p0) REVERT: H 308 ILE cc_start: 0.7756 (mt) cc_final: 0.7540 (pt) outliers start: 99 outliers final: 62 residues processed: 436 average time/residue: 0.1650 time to fit residues: 114.0698 Evaluate side-chains 396 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 327 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 368 MET Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain H residue 148 ASP Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 299 TRP Chi-restraints excluded: chain H residue 307 MET Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 253 optimal weight: 3.9990 chunk 282 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 266 optimal weight: 0.8980 chunk 281 optimal weight: 7.9990 chunk 172 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 226 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 284 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 167 ASN ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN C 57 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 HIS E 412 ASN F 355 GLN ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 9 ASN ** H 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.150851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.128421 restraints weight = 42973.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.127731 restraints weight = 31802.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.128644 restraints weight = 28300.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.129177 restraints weight = 23491.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.129363 restraints weight = 21333.130| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 24201 Z= 0.212 Angle : 0.691 12.676 32813 Z= 0.366 Chirality : 0.047 0.243 3647 Planarity : 0.005 0.055 4071 Dihedral : 10.625 166.977 3347 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.44 % Allowed : 14.74 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.15), residues: 2898 helix: 0.59 (0.13), residues: 1457 sheet: -0.70 (0.26), residues: 392 loop : -1.62 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 101 TYR 0.028 0.002 TYR F 312 PHE 0.023 0.003 PHE A 37 TRP 0.038 0.002 TRP F 428 HIS 0.008 0.002 HIS F 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.21 (24197) covalent geometry : angle 0.68528 / 0.37 (32807) hydrogen bonds : bond 0.04396 / 2.92 ( 1155) hydrogen bonds : angle 5.20334 / 3.76 ( 3303) metal coordination : bond 0.00787 / 0.39 ( 4) metal coordination : angle 6.41486 / 3.40 ( 6) *********************** 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 491 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 379 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.6568 (t0) cc_final: 0.5762 (m-30) REVERT: A 100 GLN cc_start: 0.6867 (mt0) cc_final: 0.6600 (tm-30) REVERT: A 114 GLN cc_start: 0.6767 (mt0) cc_final: 0.4932 (pt0) REVERT: A 196 MET cc_start: 0.6070 (mmt) cc_final: 0.5829 (mmp) REVERT: A 385 LEU cc_start: 0.6568 (mt) cc_final: 0.6201 (tp) REVERT: B 267 ARG cc_start: 0.6726 (OUTLIER) cc_final: 0.6280 (ttt-90) REVERT: B 418 LEU cc_start: 0.6722 (tp) cc_final: 0.6141 (tt) REVERT: C 34 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7357 (tptm) REVERT: D 1 MET cc_start: 0.6349 (ptm) cc_final: 0.5839 (ptm) REVERT: D 3 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6387 (tt0) REVERT: D 15 TYR cc_start: 0.5778 (t80) cc_final: 0.5524 (t80) REVERT: D 23 MET cc_start: 0.7238 (mmp) cc_final: 0.6900 (mmp) REVERT: D 41 LYS cc_start: 0.6716 (ttpp) cc_final: 0.6202 (pttp) REVERT: D 93 GLU cc_start: 0.6607 (mm-30) cc_final: 0.5552 (tp30) REVERT: D 303 PHE cc_start: 0.6875 (t80) cc_final: 0.6671 (t80) REVERT: E 32 PRO cc_start: 0.4944 (Cg_endo) cc_final: 0.4742 (Cg_exo) REVERT: E 43 HIS cc_start: 0.3947 (t70) cc_final: 0.3606 (t70) REVERT: E 76 LEU cc_start: 0.5970 (OUTLIER) cc_final: 0.5568 (mt) REVERT: E 124 ARG cc_start: 0.4385 (OUTLIER) cc_final: 0.4074 (ptm160) REVERT: E 131 VAL cc_start: 0.6958 (m) cc_final: 0.6708 (p) REVERT: E 331 THR cc_start: 0.6102 (m) cc_final: 0.5710 (t) REVERT: E 377 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6066 (mt) REVERT: F 75 THR cc_start: 0.6384 (p) cc_final: 0.6023 (t) REVERT: F 175 LYS cc_start: 0.5166 (tttt) cc_final: 0.4699 (tptp) REVERT: F 265 LYS cc_start: 0.7073 (mmtm) cc_final: 0.6542 (mmtp) REVERT: F 274 ARG cc_start: 0.4339 (mtm-85) cc_final: 0.3854 (mtt90) REVERT: F 384 MET cc_start: 0.5855 (mtp) cc_final: 0.5584 (ttm) REVERT: F 423 LYS cc_start: 0.6134 (mttm) cc_final: 0.5348 (mmmm) REVERT: H 18 HIS cc_start: 0.3133 (OUTLIER) cc_final: 0.2130 (p-80) REVERT: H 94 ARG cc_start: 0.5596 (OUTLIER) cc_final: 0.4940 (ttm110) REVERT: H 242 ILE cc_start: 0.5632 (mm) cc_final: 0.5221 (mm) REVERT: H 255 LEU cc_start: 0.6144 (OUTLIER) cc_final: 0.5932 (mp) REVERT: H 294 TRP cc_start: 0.7149 (m100) cc_final: 0.6733 (m100) outliers start: 112 outliers final: 77 residues processed: 465 average time/residue: 0.1582 time to fit residues: 117.7305 Evaluate side-chains 417 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 332 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 267 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 34 LYS Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 422 GLN Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 368 MET Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 412 ASN Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 299 TRP Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 334 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 181 optimal weight: 6.9990 chunk 229 optimal weight: 3.9990 chunk 36 optimal weight: 0.0770 chunk 157 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 235 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 256 optimal weight: 9.9990 chunk 261 optimal weight: 3.9990 overall best weight: 2.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN A 216 GLN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN B 200 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 ASN ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 325 ASN ** 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 = 0.4122 r_free = 0.4122 target = 0.151599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.128762 restraints weight = 43492.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.128505 restraints weight = 33005.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.129371 restraints weight = 27245.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.129785 restraints weight = 23156.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.130102 restraints weight = 20340.174| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24201 Z= 0.150 Angle : 0.608 11.268 32813 Z= 0.323 Chirality : 0.044 0.272 3647 Planarity : 0.004 0.042 4071 Dihedral : 10.529 171.666 3347 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.53 % Allowed : 16.37 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.15), residues: 2898 helix: 0.88 (0.14), residues: 1453 sheet: -0.58 (0.27), residues: 390 loop : -1.61 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 322 TYR 0.032 0.002 TYR D 165 PHE 0.020 0.002 PHE A 37 TRP 0.030 0.002 TRP F 428 HIS 0.006 0.001 HIS E 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (24197) covalent geometry : angle 0.60263 / 0.32 (32807) hydrogen bonds : bond 0.03916 / 2.60 ( 1155) hydrogen bonds : angle 5.01329 / 3.63 ( 3303) metal coordination : bond 0.00523 / 0.26 ( 4) metal coordination : angle 5.71926 / 2.95 ( 6) *********************** 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 440 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 351 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.6521 (t0) cc_final: 0.5818 (m-30) REVERT: A 80 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.6214 (mt) REVERT: A 385 LEU cc_start: 0.6527 (mt) cc_final: 0.6183 (tp) REVERT: B 103 MET cc_start: 0.7009 (mmm) cc_final: 0.5685 (mtm) REVERT: B 418 LEU cc_start: 0.6746 (tp) cc_final: 0.6157 (tt) REVERT: C 1 MET cc_start: 0.7904 (ptm) cc_final: 0.7468 (ptt) REVERT: D 1 MET cc_start: 0.6308 (ptm) cc_final: 0.5865 (ptm) REVERT: D 3 GLU cc_start: 0.6731 (mt-10) cc_final: 0.6352 (tt0) REVERT: D 23 MET cc_start: 0.7214 (mmp) cc_final: 0.6926 (mmp) REVERT: D 41 LYS cc_start: 0.6656 (ttpp) cc_final: 0.6116 (pttp) REVERT: D 48 HIS cc_start: 0.5324 (m90) cc_final: 0.4739 (m-70) REVERT: D 52 SER cc_start: 0.7036 (p) cc_final: 0.6768 (t) REVERT: D 93 GLU cc_start: 0.6589 (mm-30) cc_final: 0.5532 (tp30) REVERT: D 416 LYS cc_start: 0.6743 (OUTLIER) cc_final: 0.6519 (mmmm) REVERT: E 43 HIS cc_start: 0.3989 (t70) cc_final: 0.3600 (t70) REVERT: E 76 LEU cc_start: 0.6010 (OUTLIER) cc_final: 0.5616 (mt) REVERT: E 124 ARG cc_start: 0.4430 (OUTLIER) cc_final: 0.4113 (ptm160) REVERT: E 131 VAL cc_start: 0.6966 (m) cc_final: 0.6710 (p) REVERT: E 264 GLU cc_start: 0.5491 (mt-10) cc_final: 0.5283 (mt-10) REVERT: E 290 PHE cc_start: 0.6064 (m-80) cc_final: 0.5837 (m-80) REVERT: E 331 THR cc_start: 0.5934 (m) cc_final: 0.5568 (t) REVERT: E 377 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6105 (mt) REVERT: F 48 HIS cc_start: 0.5335 (m90) cc_final: 0.5115 (m170) REVERT: F 75 THR cc_start: 0.6336 (p) cc_final: 0.5754 (t) REVERT: F 79 LYS cc_start: 0.6832 (mttm) cc_final: 0.6603 (mmtp) REVERT: F 152 HIS cc_start: 0.6600 (t70) cc_final: 0.6267 (t-170) REVERT: F 175 LYS cc_start: 0.5253 (tttt) cc_final: 0.4646 (tptp) REVERT: F 265 LYS cc_start: 0.7016 (mmtm) cc_final: 0.6499 (mmtp) REVERT: F 274 ARG cc_start: 0.4336 (mtm-85) cc_final: 0.3866 (mtt90) REVERT: F 332 VAL cc_start: 0.5923 (t) cc_final: 0.5408 (t) REVERT: F 384 MET cc_start: 0.5649 (mtp) cc_final: 0.5384 (ttm) REVERT: F 423 LYS cc_start: 0.6112 (mttm) cc_final: 0.5372 (mmmm) REVERT: H 18 HIS cc_start: 0.3057 (OUTLIER) cc_final: 0.2075 (p-80) REVERT: H 94 ARG cc_start: 0.5588 (OUTLIER) cc_final: 0.5344 (mtp-110) REVERT: H 220 TYR cc_start: 0.5729 (t80) cc_final: 0.5289 (t80) REVERT: H 242 ILE cc_start: 0.5560 (mm) cc_final: 0.5120 (mm) REVERT: H 294 TRP cc_start: 0.7111 (m100) cc_final: 0.6723 (m100) outliers start: 89 outliers final: 69 residues processed: 419 average time/residue: 0.1628 time to fit residues: 108.7153 Evaluate side-chains 404 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 328 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 422 GLN Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 368 MET Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 299 TRP Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 334 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 270 optimal weight: 6.9990 chunk 246 optimal weight: 9.9990 chunk 286 optimal weight: 8.9990 chunk 256 optimal weight: 6.9990 chunk 269 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 145 optimal weight: 8.9990 chunk 180 optimal weight: 0.9980 chunk 191 optimal weight: 7.9990 overall best weight: 3.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN C 57 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN F 302 ASN ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 ASN H 325 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.150912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.128285 restraints weight = 43340.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.127441 restraints weight = 35939.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.128932 restraints weight = 30445.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.129350 restraints weight = 23394.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.129633 restraints weight = 20036.398| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 24201 Z= 0.173 Angle : 0.626 11.428 32813 Z= 0.333 Chirality : 0.045 0.281 3647 Planarity : 0.004 0.043 4071 Dihedral : 10.592 174.672 3347 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.88 % Allowed : 16.53 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.15), residues: 2898 helix: 0.83 (0.14), residues: 1455 sheet: -0.57 (0.27), residues: 384 loop : -1.66 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 322 TYR 0.021 0.002 TYR F 312 PHE 0.019 0.002 PHE A 37 TRP 0.028 0.002 TRP F 428 HIS 0.006 0.001 HIS F 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (24197) covalent geometry : angle 0.62057 / 0.33 (32807) hydrogen bonds : bond 0.03959 / 2.62 ( 1155) hydrogen bonds : angle 5.02695 / 3.63 ( 3303) metal coordination : bond 0.00569 / 0.28 ( 4) metal coordination : angle 6.10497 / 3.18 ( 6) *********************** 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 440 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 342 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.6532 (t0) cc_final: 0.5815 (m-30) REVERT: A 22 TYR cc_start: 0.7761 (m-80) cc_final: 0.7556 (m-80) REVERT: A 80 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.6285 (mt) REVERT: A 380 THR cc_start: 0.7290 (p) cc_final: 0.7076 (t) REVERT: B 76 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.8023 (tt) REVERT: B 267 ARG cc_start: 0.6711 (OUTLIER) cc_final: 0.6277 (ttt-90) REVERT: B 418 LEU cc_start: 0.6775 (tp) cc_final: 0.6207 (tt) REVERT: C 1 MET cc_start: 0.7889 (ptm) cc_final: 0.7411 (ptt) REVERT: D 1 MET cc_start: 0.6270 (ptm) cc_final: 0.5851 (ptm) REVERT: D 3 GLU cc_start: 0.6801 (mt-10) cc_final: 0.6398 (tt0) REVERT: D 23 MET cc_start: 0.7189 (mmp) cc_final: 0.6919 (mmp) REVERT: D 41 LYS cc_start: 0.6745 (ttpp) cc_final: 0.6232 (pttp) REVERT: D 48 HIS cc_start: 0.5361 (m90) cc_final: 0.4790 (m-70) REVERT: D 52 SER cc_start: 0.7058 (p) cc_final: 0.6818 (t) REVERT: D 93 GLU cc_start: 0.6549 (mm-30) cc_final: 0.5582 (tp30) REVERT: E 43 HIS cc_start: 0.4056 (t70) cc_final: 0.3689 (t70) REVERT: E 76 LEU cc_start: 0.6013 (OUTLIER) cc_final: 0.5613 (mt) REVERT: E 124 ARG cc_start: 0.4430 (OUTLIER) cc_final: 0.4130 (ptm160) REVERT: E 131 VAL cc_start: 0.6974 (m) cc_final: 0.6717 (p) REVERT: E 331 THR cc_start: 0.6021 (m) cc_final: 0.5680 (t) REVERT: E 377 LEU cc_start: 0.6638 (OUTLIER) cc_final: 0.6113 (mt) REVERT: F 75 THR cc_start: 0.6301 (p) cc_final: 0.5760 (t) REVERT: F 152 HIS cc_start: 0.6599 (t70) cc_final: 0.6270 (t-170) REVERT: F 175 LYS cc_start: 0.5146 (tttt) cc_final: 0.4636 (tptp) REVERT: F 265 LYS cc_start: 0.7061 (mmtm) cc_final: 0.6552 (mmtp) REVERT: F 274 ARG cc_start: 0.4330 (mtm-85) cc_final: 0.3885 (mtt90) REVERT: F 321 ILE cc_start: 0.4792 (mt) cc_final: 0.4510 (mm) REVERT: F 384 MET cc_start: 0.5686 (mtp) cc_final: 0.5405 (ttm) REVERT: F 423 LYS cc_start: 0.6132 (mttm) cc_final: 0.5429 (mmmm) REVERT: H 18 HIS cc_start: 0.3149 (OUTLIER) cc_final: 0.2143 (p-80) REVERT: H 94 ARG cc_start: 0.5619 (OUTLIER) cc_final: 0.5393 (mtp-110) REVERT: H 242 ILE cc_start: 0.5539 (mm) cc_final: 0.5122 (mm) REVERT: H 294 TRP cc_start: 0.7133 (m100) cc_final: 0.6707 (m100) outliers start: 98 outliers final: 77 residues processed: 418 average time/residue: 0.1643 time to fit residues: 109.6401 Evaluate side-chains 417 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 332 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 267 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 422 GLN Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 368 MET Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain H residue 148 ASP Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 299 TRP Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 307 MET Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 334 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 47 optimal weight: 0.5980 chunk 247 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 237 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN A 403 GLN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN B 200 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 ASN ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.152622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.130543 restraints weight = 43042.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.129607 restraints weight = 34150.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.131069 restraints weight = 25529.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.131807 restraints weight = 20956.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.131873 restraints weight = 18903.861| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.5436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24201 Z= 0.121 Angle : 0.576 9.929 32813 Z= 0.305 Chirality : 0.042 0.283 3647 Planarity : 0.004 0.038 4071 Dihedral : 10.450 179.124 3347 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.77 % Allowed : 17.36 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.16), residues: 2898 helix: 1.14 (0.14), residues: 1456 sheet: -0.44 (0.28), residues: 390 loop : -1.59 (0.17), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 236 TYR 0.019 0.001 TYR A 165 PHE 0.021 0.002 PHE F 174 TRP 0.026 0.002 TRP F 428 HIS 0.008 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (24197) covalent geometry : angle 0.57148 / 0.31 (32807) hydrogen bonds : bond 0.03503 / 2.31 ( 1155) hydrogen bonds : angle 4.82632 / 3.49 ( 3303) metal coordination : bond 0.00301 / 0.15 ( 4) metal coordination : angle 5.33314 / 2.68 ( 6) *********************** 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 437 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 367 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.6455 (t0) cc_final: 0.5794 (m-30) REVERT: A 80 LEU cc_start: 0.6501 (OUTLIER) cc_final: 0.6213 (mt) REVERT: A 380 THR cc_start: 0.7139 (p) cc_final: 0.6916 (t) REVERT: B 267 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.6221 (ttt-90) REVERT: B 338 GLU cc_start: 0.6225 (mt-10) cc_final: 0.5402 (mm-30) REVERT: B 418 LEU cc_start: 0.6748 (tp) cc_final: 0.6173 (tt) REVERT: C 1 MET cc_start: 0.7897 (ptm) cc_final: 0.7474 (ptt) REVERT: C 263 MET cc_start: 0.6652 (mmm) cc_final: 0.5976 (mtp) REVERT: C 400 LEU cc_start: 0.6897 (tp) cc_final: 0.6658 (tt) REVERT: D 1 MET cc_start: 0.6206 (ptm) cc_final: 0.5826 (ptm) REVERT: D 3 GLU cc_start: 0.6771 (mt-10) cc_final: 0.6434 (tt0) REVERT: D 23 MET cc_start: 0.7134 (mmp) cc_final: 0.6875 (mmp) REVERT: D 41 LYS cc_start: 0.6706 (ttpp) cc_final: 0.6163 (pttp) REVERT: D 48 HIS cc_start: 0.5400 (m90) cc_final: 0.4845 (m-70) REVERT: D 52 SER cc_start: 0.7066 (p) cc_final: 0.6828 (t) REVERT: D 93 GLU cc_start: 0.6560 (mm-30) cc_final: 0.5609 (tp30) REVERT: E 43 HIS cc_start: 0.4143 (t70) cc_final: 0.3837 (t70) REVERT: E 76 LEU cc_start: 0.6020 (OUTLIER) cc_final: 0.5600 (mt) REVERT: E 124 ARG cc_start: 0.4431 (OUTLIER) cc_final: 0.4088 (ptm160) REVERT: E 131 VAL cc_start: 0.6976 (m) cc_final: 0.6710 (p) REVERT: E 331 THR cc_start: 0.5880 (m) cc_final: 0.5565 (t) REVERT: E 377 LEU cc_start: 0.6619 (OUTLIER) cc_final: 0.6044 (mt) REVERT: E 391 GLU cc_start: 0.6009 (pt0) cc_final: 0.5691 (pt0) REVERT: F 75 THR cc_start: 0.6265 (p) cc_final: 0.5765 (t) REVERT: F 152 HIS cc_start: 0.6574 (t70) cc_final: 0.6193 (t-170) REVERT: F 166 MET cc_start: 0.5343 (mmt) cc_final: 0.5133 (mmm) REVERT: F 175 LYS cc_start: 0.5202 (tttt) cc_final: 0.4646 (tptp) REVERT: F 265 LYS cc_start: 0.7022 (mmtm) cc_final: 0.6513 (mmtp) REVERT: F 274 ARG cc_start: 0.4284 (mtm-85) cc_final: 0.3847 (mtt90) REVERT: F 321 ILE cc_start: 0.4782 (mt) cc_final: 0.4464 (mm) REVERT: F 332 VAL cc_start: 0.5954 (t) cc_final: 0.5440 (t) REVERT: F 423 LYS cc_start: 0.6049 (mttm) cc_final: 0.5404 (mmmm) REVERT: H 18 HIS cc_start: 0.3059 (OUTLIER) cc_final: 0.2140 (p-80) REVERT: H 49 LYS cc_start: 0.1606 (mttt) cc_final: 0.1236 (tptp) REVERT: H 92 GLU cc_start: 0.5447 (tp30) cc_final: 0.4704 (tp30) REVERT: H 94 ARG cc_start: 0.5642 (OUTLIER) cc_final: 0.5375 (mtp-110) REVERT: H 242 ILE cc_start: 0.5502 (mm) cc_final: 0.5109 (mm) REVERT: H 294 TRP cc_start: 0.7037 (m100) cc_final: 0.6651 (m100) outliers start: 70 outliers final: 46 residues processed: 419 average time/residue: 0.1668 time to fit residues: 110.9498 Evaluate side-chains 387 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 334 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain B residue 267 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 422 GLN Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 299 TRP Chi-restraints excluded: chain H residue 307 MET Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 121 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 276 optimal weight: 10.0000 chunk 112 optimal weight: 0.5980 chunk 174 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 281 optimal weight: 6.9990 chunk 242 optimal weight: 20.0000 chunk 115 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN A 403 GLN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 ASN ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.152788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.130735 restraints weight = 43152.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.129710 restraints weight = 32968.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.130617 restraints weight = 26204.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.131197 restraints weight = 24193.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.131457 restraints weight = 20765.484| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24201 Z= 0.122 Angle : 0.576 11.349 32813 Z= 0.305 Chirality : 0.042 0.274 3647 Planarity : 0.004 0.077 4071 Dihedral : 10.391 179.826 3345 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.46 % Allowed : 17.99 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.16), residues: 2898 helix: 1.16 (0.14), residues: 1458 sheet: -0.32 (0.28), residues: 390 loop : -1.56 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 87 TYR 0.023 0.001 TYR F 15 PHE 0.024 0.002 PHE H 241 TRP 0.033 0.002 TRP H 53 HIS 0.015 0.001 HIS F 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (24197) covalent geometry : angle 0.57128 / 0.30 (32807) hydrogen bonds : bond 0.03454 / 2.29 ( 1155) hydrogen bonds : angle 4.77030 / 3.45 ( 3303) metal coordination : bond 0.00299 / 0.15 ( 4) metal coordination : angle 5.28389 / 2.66 ( 6) *********************** 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 409 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 347 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.6476 (t0) cc_final: 0.5819 (m-30) REVERT: A 80 LEU cc_start: 0.6480 (OUTLIER) cc_final: 0.6193 (mt) REVERT: A 380 THR cc_start: 0.7094 (p) cc_final: 0.6893 (t) REVERT: B 89 TRP cc_start: 0.6715 (t60) cc_final: 0.6436 (t60) REVERT: B 163 LEU cc_start: 0.7367 (mm) cc_final: 0.6736 (tp) REVERT: B 267 ARG cc_start: 0.6639 (OUTLIER) cc_final: 0.6210 (ttt-90) REVERT: B 338 GLU cc_start: 0.6357 (mt-10) cc_final: 0.5312 (mm-30) REVERT: C 1 MET cc_start: 0.7873 (ptm) cc_final: 0.7500 (ptt) REVERT: C 159 GLU cc_start: 0.6413 (mm-30) cc_final: 0.6041 (tt0) REVERT: C 400 LEU cc_start: 0.6892 (tp) cc_final: 0.6690 (tt) REVERT: D 1 MET cc_start: 0.6178 (ptm) cc_final: 0.5764 (ptm) REVERT: D 3 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6425 (tt0) REVERT: D 23 MET cc_start: 0.7150 (mmp) cc_final: 0.6893 (mmp) REVERT: D 41 LYS cc_start: 0.6729 (ttpp) cc_final: 0.6211 (pttp) REVERT: D 48 HIS cc_start: 0.5393 (m90) cc_final: 0.4857 (m-70) REVERT: D 52 SER cc_start: 0.7070 (p) cc_final: 0.6840 (t) REVERT: D 93 GLU cc_start: 0.6543 (mm-30) cc_final: 0.5668 (tp30) REVERT: E 18 LYS cc_start: 0.5911 (mmtm) cc_final: 0.5225 (tptt) REVERT: E 43 HIS cc_start: 0.4214 (t70) cc_final: 0.3894 (t70) REVERT: E 76 LEU cc_start: 0.6042 (OUTLIER) cc_final: 0.5578 (mt) REVERT: E 124 ARG cc_start: 0.4406 (OUTLIER) cc_final: 0.4056 (ptm160) REVERT: E 131 VAL cc_start: 0.6950 (m) cc_final: 0.6691 (p) REVERT: E 299 LEU cc_start: 0.5907 (OUTLIER) cc_final: 0.5642 (tt) REVERT: E 331 THR cc_start: 0.5884 (m) cc_final: 0.5567 (t) REVERT: E 377 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.6039 (mt) REVERT: E 391 GLU cc_start: 0.6053 (pt0) cc_final: 0.5742 (pt0) REVERT: F 1 MET cc_start: 0.5787 (OUTLIER) cc_final: 0.5538 (ptt) REVERT: F 166 MET cc_start: 0.5432 (mmt) cc_final: 0.5188 (mmm) REVERT: F 175 LYS cc_start: 0.5252 (tttt) cc_final: 0.4685 (tptp) REVERT: F 265 LYS cc_start: 0.7040 (mmtm) cc_final: 0.6516 (mmtp) REVERT: F 274 ARG cc_start: 0.4405 (mtm-85) cc_final: 0.3846 (mtt90) REVERT: F 321 ILE cc_start: 0.4768 (mt) cc_final: 0.4468 (mp) REVERT: F 332 VAL cc_start: 0.5864 (t) cc_final: 0.5381 (t) REVERT: F 384 MET cc_start: 0.5624 (mtp) cc_final: 0.5223 (ttm) REVERT: F 423 LYS cc_start: 0.6048 (mttm) cc_final: 0.5406 (mmmm) REVERT: H 18 HIS cc_start: 0.3158 (OUTLIER) cc_final: 0.2258 (p-80) REVERT: H 49 LYS cc_start: 0.1595 (mttt) cc_final: 0.1261 (tptp) REVERT: H 92 GLU cc_start: 0.5415 (tp30) cc_final: 0.4622 (tp30) REVERT: H 242 ILE cc_start: 0.5532 (mm) cc_final: 0.5136 (mm) REVERT: H 294 TRP cc_start: 0.7037 (m100) cc_final: 0.6637 (m100) outliers start: 62 outliers final: 47 residues processed: 397 average time/residue: 0.1690 time to fit residues: 105.8912 Evaluate side-chains 389 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 334 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 267 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 422 GLN Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 148 ASP Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 299 TRP Chi-restraints excluded: chain H residue 307 MET Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 83 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 208 optimal weight: 0.9980 chunk 241 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 184 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 ASN ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.153529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.130377 restraints weight = 43233.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.130385 restraints weight = 32883.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.131082 restraints weight = 26491.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.131787 restraints weight = 22748.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.132158 restraints weight = 19792.299| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.5619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 24201 Z= 0.115 Angle : 0.571 11.648 32813 Z= 0.300 Chirality : 0.042 0.273 3647 Planarity : 0.004 0.051 4071 Dihedral : 10.276 176.350 3345 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.38 % Allowed : 18.15 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.16), residues: 2898 helix: 1.24 (0.14), residues: 1459 sheet: -0.28 (0.28), residues: 389 loop : -1.53 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 236 TYR 0.030 0.001 TYR D 15 PHE 0.021 0.002 PHE H 241 TRP 0.024 0.001 TRP H 266 HIS 0.010 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (24197) covalent geometry : angle 0.56727 / 0.30 (32807) hydrogen bonds : bond 0.03293 / 2.19 ( 1155) hydrogen bonds : angle 4.69795 / 3.40 ( 3303) metal coordination : bond 0.00219 / 0.11 ( 4) metal coordination : angle 5.13082 / 2.54 ( 6) ********************** 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 420 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 360 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6622 (tpp) cc_final: 0.6317 (tpp) REVERT: A 12 ASP cc_start: 0.6466 (t0) cc_final: 0.5854 (m-30) REVERT: A 80 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.6052 (mt) REVERT: B 163 LEU cc_start: 0.7323 (mm) cc_final: 0.6731 (tp) REVERT: B 267 ARG cc_start: 0.6615 (OUTLIER) cc_final: 0.6181 (ttt-90) REVERT: B 326 GLU cc_start: 0.4928 (tt0) cc_final: 0.4698 (tt0) REVERT: B 338 GLU cc_start: 0.6223 (mt-10) cc_final: 0.5402 (mm-30) REVERT: C 1 MET cc_start: 0.7843 (ptm) cc_final: 0.7474 (ptt) REVERT: C 159 GLU cc_start: 0.6407 (mm-30) cc_final: 0.6093 (tt0) REVERT: C 400 LEU cc_start: 0.6877 (tp) cc_final: 0.6655 (tt) REVERT: D 1 MET cc_start: 0.6161 (ptm) cc_final: 0.5767 (ptm) REVERT: D 3 GLU cc_start: 0.6757 (mt-10) cc_final: 0.6407 (tt0) REVERT: D 23 MET cc_start: 0.7076 (mmp) cc_final: 0.6834 (mmp) REVERT: D 41 LYS cc_start: 0.6732 (ttpp) cc_final: 0.6220 (pttp) REVERT: D 48 HIS cc_start: 0.5259 (m90) cc_final: 0.4875 (m-70) REVERT: D 52 SER cc_start: 0.7038 (p) cc_final: 0.6791 (t) REVERT: D 93 GLU cc_start: 0.6494 (mm-30) cc_final: 0.5670 (tp30) REVERT: D 373 GLU cc_start: 0.4382 (pm20) cc_final: 0.4170 (pm20) REVERT: E 18 LYS cc_start: 0.5851 (mmtm) cc_final: 0.5175 (tptt) REVERT: E 43 HIS cc_start: 0.4197 (t70) cc_final: 0.3869 (t70) REVERT: E 76 LEU cc_start: 0.6067 (OUTLIER) cc_final: 0.5568 (mm) REVERT: E 124 ARG cc_start: 0.4339 (OUTLIER) cc_final: 0.3979 (ptm160) REVERT: E 131 VAL cc_start: 0.6950 (m) cc_final: 0.6680 (p) REVERT: E 246 LEU cc_start: 0.6836 (tp) cc_final: 0.6626 (tp) REVERT: E 331 THR cc_start: 0.5841 (m) cc_final: 0.5497 (t) REVERT: E 377 LEU cc_start: 0.6582 (OUTLIER) cc_final: 0.6054 (mt) REVERT: E 391 GLU cc_start: 0.6013 (pt0) cc_final: 0.5732 (pt0) REVERT: F 1 MET cc_start: 0.5721 (OUTLIER) cc_final: 0.5514 (ptt) REVERT: F 175 LYS cc_start: 0.5332 (tttt) cc_final: 0.4743 (tptp) REVERT: F 265 LYS cc_start: 0.7048 (mmtm) cc_final: 0.6522 (mmtp) REVERT: F 274 ARG cc_start: 0.4419 (mtm-85) cc_final: 0.3844 (mtt90) REVERT: F 332 VAL cc_start: 0.5861 (t) cc_final: 0.5380 (t) REVERT: F 384 MET cc_start: 0.5685 (mtp) cc_final: 0.5316 (ttm) REVERT: F 423 LYS cc_start: 0.5969 (mttm) cc_final: 0.5379 (mmmm) REVERT: H 8 ASP cc_start: 0.5270 (m-30) cc_final: 0.4531 (t0) REVERT: H 18 HIS cc_start: 0.3074 (OUTLIER) cc_final: 0.2216 (p-80) REVERT: H 49 LYS cc_start: 0.1654 (mttt) cc_final: 0.1287 (tptp) REVERT: H 92 GLU cc_start: 0.5537 (tp30) cc_final: 0.4664 (tp30) REVERT: H 242 ILE cc_start: 0.5490 (mm) cc_final: 0.5115 (mm) REVERT: H 294 TRP cc_start: 0.7022 (m100) cc_final: 0.6647 (m100) outliers start: 60 outliers final: 43 residues processed: 406 average time/residue: 0.1610 time to fit residues: 103.6194 Evaluate side-chains 386 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 336 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 267 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 422 GLN Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 148 ASP Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 299 TRP Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 48 optimal weight: 0.9980 chunk 273 optimal weight: 8.9990 chunk 226 optimal weight: 2.9990 chunk 251 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 265 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 206 optimal weight: 0.9990 chunk 235 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN B 425 ASN ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 GLN F 302 ASN ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.151888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.129632 restraints weight = 43638.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.128727 restraints weight = 34069.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.129341 restraints weight = 30711.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.130045 restraints weight = 25082.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.130327 restraints weight = 21535.778| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24201 Z= 0.125 Angle : 0.583 11.816 32813 Z= 0.308 Chirality : 0.043 0.281 3647 Planarity : 0.004 0.059 4071 Dihedral : 10.264 175.065 3345 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.34 % Allowed : 18.55 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.16), residues: 2898 helix: 1.24 (0.14), residues: 1451 sheet: -0.36 (0.28), residues: 395 loop : -1.58 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 236 TYR 0.028 0.001 TYR D 312 PHE 0.030 0.002 PHE H 194 TRP 0.031 0.002 TRP H 53 HIS 0.014 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (24197) covalent geometry : angle 0.57825 / 0.31 (32807) hydrogen bonds : bond 0.03371 / 2.24 ( 1155) hydrogen bonds : angle 4.70630 / 3.40 ( 3303) metal coordination : bond 0.00284 / 0.14 ( 4) metal coordination : angle 5.28386 / 2.65 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4224.70 seconds wall clock time: 74 minutes 20.22 seconds (4460.22 seconds total)