Starting phenix.real_space_refine on Sat Jul 4 12:00:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g0z_29658/07_2026/8g0z_29658.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g0z_29658/07_2026/8g0z_29658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g0z_29658/07_2026/8g0z_29658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g0z_29658/07_2026/8g0z_29658.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8g0z_29658/07_2026/8g0z_29658.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g0z_29658/07_2026/8g0z_29658.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g0z_29658/07_2026/8g0z_29658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g0z_29658/07_2026/8g0z_29658.map" } resolution = 3.61 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 27 5.49 5 Mg 5 5.21 5 S 119 5.16 5 C 13244 2.51 5 N 3475 2.21 5 O 4074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20944 Number of models: 1 Model: "" Number of chains: 12 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: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.22, per 1000 atoms: 0.25 Number of scatterers: 20944 At special positions: 0 Unit cell: (140.973, 136.857, 143.031, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 119 16.00 P 27 15.00 Mg 5 11.99 O 4074 8.00 N 3475 7.00 C 13244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 1.1 seconds 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4920 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 15 sheets defined 55.6% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 Processing helix chain 'A' and resid 13 through 20 Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 24 through 28 Processing helix chain 'A' and resid 31 through 47 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 66 through 79 Processing helix chain 'A' and resid 86 through 118 Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 176 through 183 Processing helix chain 'A' and resid 204 through 217 removed outlier: 3.636A pdb=" N TYR A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 243 Processing helix chain 'A' and resid 245 through 252 removed outlier: 3.519A pdb=" N ILE A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 269 removed outlier: 3.550A pdb=" N LYS A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 301 Processing helix chain 'A' and resid 328 through 347 Processing helix chain 'A' and resid 357 through 363 Processing helix chain 'A' and resid 390 through 396 Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'B' and resid 12 through 20 Processing helix chain 'B' and resid 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 24 through 28 removed outlier: 3.543A pdb=" N TYR B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE B 28 " --> pdb=" O SER B 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 24 through 28' Processing helix chain 'B' and resid 31 through 48 Processing helix chain 'B' and resid 52 through 58 Processing helix chain 'B' and resid 66 through 80 Processing helix chain 'B' and resid 88 through 119 removed outlier: 3.529A pdb=" N LEU B 119 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 133 Processing helix chain 'B' and resid 134 through 143 Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 176 through 184 removed outlier: 3.512A pdb=" N ILE B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 217 Processing helix chain 'B' and resid 229 through 243 removed outlier: 3.767A pdb=" N CYS B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA B 234 " --> pdb=" O GLU B 230 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 286 through 301 Processing helix chain 'B' and resid 327 through 347 removed outlier: 3.589A pdb=" N THR B 331 " --> pdb=" O ASN B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'B' and resid 391 through 396 removed outlier: 3.628A pdb=" N ALA B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 13 through 20 Processing helix chain 'C' and resid 24 through 28 removed outlier: 3.769A pdb=" N PHE C 28 " --> pdb=" O SER C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 47 Processing helix chain 'C' and resid 52 through 63 Processing helix chain 'C' and resid 66 through 77 removed outlier: 4.001A pdb=" N GLY C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 119 Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 133 through 143 Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 230 through 242 Processing helix chain 'C' and resid 245 through 252 Processing helix chain 'C' and resid 255 through 268 Processing helix chain 'C' and resid 286 through 301 Processing helix chain 'C' and resid 312 through 316 removed outlier: 3.640A pdb=" N ILE C 315 " --> pdb=" O TYR C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 347 Processing helix chain 'C' and resid 357 through 361 removed outlier: 3.653A pdb=" N TRP C 361 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 375 through 381 removed outlier: 3.956A 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: 3.609A pdb=" N LYS D 18 " --> pdb=" O ALA D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 23 No H-bonds generated for 'chain 'D' and resid 21 through 23' Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.502A pdb=" N TYR D 27 " --> pdb=" O ASP D 24 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE D 28 " --> pdb=" O SER D 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 24 through 28' Processing helix chain 'D' and resid 31 through 48 Processing helix chain 'D' and resid 52 through 62 Processing helix chain 'D' and resid 66 through 80 Processing helix chain 'D' and resid 86 through 118 Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 133 through 143 removed outlier: 3.935A 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 removed outlier: 3.811A pdb=" N CYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) 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: 4.005A pdb=" N ALA D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 396 Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 12 through 20 removed outlier: 3.593A pdb=" N LYS E 18 " --> pdb=" O ALA E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 28 removed outlier: 3.560A pdb=" N PHE E 28 " --> pdb=" O SER E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 47 Processing helix chain 'E' and resid 52 through 63 Processing helix chain 'E' and resid 66 through 79 Processing helix chain 'E' and resid 86 through 118 Processing helix chain 'E' and resid 130 through 132 No H-bonds generated for 'chain 'E' and resid 130 through 132' Processing helix chain 'E' and resid 133 through 141 removed outlier: 3.695A 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 removed outlier: 3.724A pdb=" N CYS E 233 " --> pdb=" O ALA E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 251 removed outlier: 3.587A pdb=" N ASP E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 269 Processing helix chain 'E' and resid 286 through 301 Processing helix chain 'E' and resid 327 through 347 removed outlier: 3.842A pdb=" N LYS E 333 " --> pdb=" O TYR E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 361 Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 390 through 397 Processing helix chain 'F' and resid 2 through 12 Processing helix chain 'F' and resid 13 through 20 Processing helix chain 'F' and resid 21 through 23 No H-bonds generated for 'chain 'F' and resid 21 through 23' Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 31 through 48 removed outlier: 3.759A 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: 3.902A 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 300 Processing helix chain 'F' and resid 327 through 347 Processing helix chain 'F' and resid 376 through 381 Processing sheet with id=AA1, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA2, first strand: chain 'A' and resid 427 through 429 removed outlier: 3.674A pdb=" N LEU A 400 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE A 388 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N MET A 384 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 383 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA A 353 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU A 222 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 221 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LYS A 278 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TYR A 223 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, 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: 6.241A pdb=" N TYR C 223 " --> pdb=" O LYS C 278 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ASN C 220 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ILE C 309 " --> pdb=" O ASN C 220 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU C 222 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 3.934A 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: 6.430A pdb=" N MET C 384 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 171 through 172 Processing sheet with id=AA5, first strand: chain 'B' and resid 275 through 279 removed outlier: 6.563A pdb=" N VAL B 221 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LYS B 278 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR B 223 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU B 222 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 353 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B 383 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS B 405 " --> pdb=" O MET B 384 " (cutoff:3.500A) Processing sheet with id=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: 7.748A pdb=" N LYS D 278 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR D 223 " --> pdb=" O LYS D 278 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ILE D 309 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU D 222 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 171 through 172 Processing sheet with id=AA9, first strand: chain 'C' and resid 398 through 399 Processing sheet with id=AB1, first strand: chain 'D' and resid 152 through 153 removed outlier: 3.875A pdb=" N ALA E 353 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA E 354 " --> pdb=" O LEU E 195 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU E 192 " --> pdb=" O PHE E 383 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N LEU E 385 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL E 194 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 7.860A 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: 6.501A 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: 6.345A pdb=" N ASN D 193 " --> pdb=" O THR D 352 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ALA D 354 " --> pdb=" O ASN D 193 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU D 195 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU D 192 " --> pdb=" O PHE D 383 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N LEU D 385 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL D 194 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL D 387 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N MET D 196 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N MET D 384 " --> pdb=" O ILE D 404 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 171 through 172 Processing sheet with id=AB5, first strand: chain 'F' and resid 275 through 279 removed outlier: 6.986A pdb=" N LEU F 222 " --> pdb=" O ILE F 309 " (cutoff:3.500A) 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 419 through 422 1054 hydrogen bonds defined for protein. 3030 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.66 Time building geometry restraints manager: 2.63 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: 6695 1.35 - 1.50: 5604 1.50 - 1.65: 8860 1.65 - 1.80: 95 1.80 - 1.95: 114 Bond restraints: 21368 Sorted by residual: bond pdb=" N ILE A 321 " pdb=" CA ILE A 321 " ideal model delta sigma weight residual 1.460 1.494 -0.034 8.60e-03 1.35e+04 1.54e+01 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 1.50e+01 bond pdb=" CE1 HIS B 152 " pdb=" NE2 HIS B 152 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.23e+01 bond pdb=" C3' DT M 16 " pdb=" C2' DT M 16 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" N VAL E 19 " pdb=" CA VAL E 19 " ideal model delta sigma weight residual 1.452 1.492 -0.040 1.18e-02 7.18e+03 1.14e+01 ... (remaining 21363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 28436 2.53 - 5.06: 498 5.06 - 7.59: 24 7.59 - 10.13: 4 10.13 - 12.66: 4 Bond angle restraints: 28966 Sorted by residual: angle pdb=" N ILE A 321 " pdb=" CA ILE A 321 " pdb=" C ILE A 321 " ideal model delta sigma weight residual 113.71 107.76 5.95 9.50e-01 1.11e+00 3.92e+01 angle pdb=" N MET C 226 " pdb=" CA MET C 226 " pdb=" C MET C 226 " ideal model delta sigma weight residual 112.54 107.17 5.37 1.22e+00 6.72e-01 1.94e+01 angle pdb=" PB AGS C 501 " pdb=" O3B AGS C 501 " pdb=" PG AGS C 501 " ideal model delta sigma weight residual 120.12 132.78 -12.66 3.00e+00 1.11e-01 1.78e+01 angle pdb=" N3 DT M 6 " pdb=" C4 DT M 6 " pdb=" O4 DT M 6 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT M 11 " pdb=" C4 DT M 11 " pdb=" O4 DT M 11 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 28961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 12711 34.84 - 69.67: 153 69.67 - 104.51: 8 104.51 - 139.35: 1 139.35 - 174.18: 3 Dihedral angle restraints: 12876 sinusoidal: 5262 harmonic: 7614 Sorted by residual: 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 -67.73 106.45 -174.18 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 -88.55 157.46 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" O1A AGS D 501 " pdb=" O3A AGS D 501 " pdb=" PA AGS D 501 " pdb=" PB AGS D 501 " ideal model delta sinusoidal sigma weight residual -67.73 66.55 -134.28 1 3.00e+01 1.11e-03 1.81e+01 ... (remaining 12873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2305 0.044 - 0.088: 576 0.088 - 0.132: 276 0.132 - 0.176: 66 0.176 - 0.220: 23 Chirality restraints: 3246 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 1.21e+00 chirality pdb=" CA ILE A 388 " pdb=" N ILE A 388 " pdb=" C ILE A 388 " pdb=" CB ILE A 388 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.16e+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 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 3243 not shown) Planarity restraints: 3599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 373 " 0.016 2.00e-02 2.50e+03 3.35e-02 1.12e+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 5.12e+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 SER B 255 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.92e+00 pdb=" C SER B 255 " 0.038 2.00e-02 2.50e+03 pdb=" O SER B 255 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR B 256 " -0.013 2.00e-02 2.50e+03 ... (remaining 3596 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 81 2.44 - 3.06: 14201 3.06 - 3.67: 31753 3.67 - 4.29: 49152 4.29 - 4.90: 80760 Nonbonded interactions: 175947 Sorted by model distance: nonbonded pdb=" O3G AGS F 501 " pdb="MG MG F 502 " model vdw 1.829 2.170 nonbonded pdb=" O2B AGS F 501 " pdb="MG MG F 502 " model vdw 2.157 2.170 nonbonded pdb=" O2B AGS D 501 " pdb="MG MG D 502 " model vdw 2.172 2.170 nonbonded pdb=" O3G AGS C 501 " pdb="MG MG C 502 " model vdw 2.188 2.170 nonbonded pdb=" O LEU C 179 " pdb=" OG1 THR C 183 " model vdw 2.208 3.040 ... (remaining 175942 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.600 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5946 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 : 0.005 0.052 21368 Z= 0.373 Angle : 0.749 12.657 28966 Z= 0.520 Chirality : 0.052 0.220 3246 Planarity : 0.004 0.075 3599 Dihedral : 11.860 174.183 7956 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.19 % Allowed : 6.52 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.17), residues: 2580 helix: 1.37 (0.15), residues: 1308 sheet: -0.45 (0.30), residues: 342 loop : -1.31 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 291 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 0.00513 / 0.37 (21368) covalent geometry : angle 0.74897 / 0.52 (28966) hydrogen bonds : bond 0.16624 / 11.44 ( 1054) hydrogen bonds : angle 6.57383 / 4.69 ( 3030) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 435 time to evaluate : 0.738 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 333 LYS cc_start: 0.4831 (OUTLIER) cc_final: 0.4479 (tmmt) REVERT: B 43 HIS cc_start: 0.6385 (t-90) cc_final: 0.6124 (t-90) REVERT: B 155 MET cc_start: 0.6828 (tpp) cc_final: 0.6008 (ptt) REVERT: B 166 MET cc_start: 0.7525 (ptm) cc_final: 0.6856 (tpp) REVERT: B 181 LYS cc_start: 0.6950 (pttt) cc_final: 0.6451 (pptt) REVERT: D 43 HIS cc_start: 0.6779 (t-90) cc_final: 0.6517 (t-90) REVERT: D 138 MET cc_start: 0.6987 (mmm) cc_final: 0.6746 (mmm) REVERT: D 355 GLN cc_start: 0.7522 (mm-40) cc_final: 0.7159 (mm-40) REVERT: E 228 MET cc_start: 0.7540 (mtm) cc_final: 0.7307 (mtt) REVERT: E 355 GLN cc_start: 0.6268 (mm-40) cc_final: 0.6039 (mm-40) REVERT: E 380 THR cc_start: 0.6756 (OUTLIER) cc_final: 0.6465 (p) REVERT: E 388 ILE cc_start: 0.6532 (OUTLIER) cc_final: 0.6186 (pt) REVERT: F 165 TYR cc_start: 0.6930 (m-10) cc_final: 0.6185 (m-10) REVERT: F 326 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7084 (mm-30) REVERT: F 418 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.6323 (mp) REVERT: F 423 LYS cc_start: 0.6995 (mttm) cc_final: 0.6595 (mttp) outliers start: 49 outliers final: 4 residues processed: 474 average time/residue: 0.1384 time to fit residues: 101.1997 Evaluate side-chains 264 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 256 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 418 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 258 optimal weight: 20.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN A 167 ASN A 355 GLN B 227 GLN B 426 GLN C 114 GLN C 227 GLN D 116 ASN D 200 ASN D 227 GLN D 422 GLN E 412 ASN F 43 HIS ** F 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.233000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.215243 restraints weight = 21050.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.214453 restraints weight = 31914.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.214494 restraints weight = 25251.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.210973 restraints weight = 13393.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.211631 restraints weight = 14245.205| |-----------------------------------------------------------------------------| r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 21368 Z= 0.214 Angle : 0.702 9.070 28966 Z= 0.374 Chirality : 0.047 0.268 3246 Planarity : 0.005 0.040 3599 Dihedral : 10.372 172.112 2956 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.22 % Allowed : 11.26 % Favored : 85.52 % 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: -0.26 (0.17), residues: 2580 helix: 0.87 (0.14), residues: 1341 sheet: -0.81 (0.29), residues: 339 loop : -1.44 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 236 TYR 0.034 0.002 TYR C 223 PHE 0.031 0.003 PHE E 11 TRP 0.024 0.002 TRP E 266 HIS 0.006 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (21368) covalent geometry : angle 0.70163 / 0.37 (28966) hydrogen bonds : bond 0.04064 / 2.69 ( 1054) hydrogen bonds : angle 5.14274 / 3.63 ( 3030) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 317 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.6636 (tpp) cc_final: 0.6050 (tpt) REVERT: A 333 LYS cc_start: 0.5835 (OUTLIER) cc_final: 0.5131 (ttpt) REVERT: B 8 HIS cc_start: 0.7128 (m90) cc_final: 0.6912 (m-70) REVERT: B 138 MET cc_start: 0.6781 (mmp) cc_final: 0.6461 (mmm) REVERT: C 168 LYS cc_start: 0.6738 (mptt) cc_final: 0.6444 (mmmt) REVERT: C 204 SER cc_start: 0.8032 (OUTLIER) cc_final: 0.7638 (m) REVERT: D 23 MET cc_start: 0.8073 (mmm) cc_final: 0.7823 (mmt) REVERT: D 43 HIS cc_start: 0.7227 (t-90) cc_final: 0.6845 (t-90) REVERT: E 80 LEU cc_start: 0.5232 (OUTLIER) cc_final: 0.4979 (mt) REVERT: E 158 TYR cc_start: 0.5380 (p90) cc_final: 0.4958 (p90) REVERT: E 228 MET cc_start: 0.7488 (mtm) cc_final: 0.7278 (mtt) REVERT: F 3 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6609 (mm-30) REVERT: F 112 GLU cc_start: 0.6068 (OUTLIER) cc_final: 0.5748 (mp0) REVERT: F 155 MET cc_start: 0.5863 (ptt) cc_final: 0.5379 (ptt) REVERT: F 165 TYR cc_start: 0.6938 (m-10) cc_final: 0.6136 (m-10) REVERT: F 280 TYR cc_start: 0.6008 (OUTLIER) cc_final: 0.4352 (t80) REVERT: F 418 LEU cc_start: 0.6315 (OUTLIER) cc_final: 0.6076 (mp) outliers start: 72 outliers final: 33 residues processed: 371 average time/residue: 0.1269 time to fit residues: 75.2024 Evaluate side-chains 296 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 257 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 280 TYR Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 418 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 147 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 252 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 176 optimal weight: 8.9990 chunk 258 optimal weight: 20.0000 chunk 62 optimal weight: 0.6980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 ASN B 105 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN D 13 GLN D 200 ASN F 288 ASN F 398 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.209396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.194443 restraints weight = 21080.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.186879 restraints weight = 33582.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.183760 restraints weight = 23567.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.184625 restraints weight = 21224.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.185601 restraints weight = 16382.781| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 21368 Z= 0.213 Angle : 0.692 9.433 28966 Z= 0.365 Chirality : 0.047 0.229 3246 Planarity : 0.004 0.061 3599 Dihedral : 10.403 171.993 2950 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.66 % Allowed : 13.18 % Favored : 83.15 % 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: -0.58 (0.17), residues: 2580 helix: 0.69 (0.14), residues: 1338 sheet: -1.32 (0.27), residues: 351 loop : -1.54 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 236 TYR 0.026 0.002 TYR C 223 PHE 0.020 0.002 PHE F 383 TRP 0.037 0.003 TRP E 162 HIS 0.012 0.002 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 (21368) covalent geometry : angle 0.69180 / 0.37 (28966) hydrogen bonds : bond 0.04341 / 2.94 ( 1054) hydrogen bonds : angle 5.11607 / 3.61 ( 3030) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 339 time to evaluate : 0.802 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 167 ASN cc_start: 0.7654 (t0) cc_final: 0.7450 (t0) REVERT: A 333 LYS cc_start: 0.6063 (OUTLIER) cc_final: 0.5362 (ttpt) REVERT: A 345 GLU cc_start: 0.6232 (tp30) cc_final: 0.5978 (tp30) REVERT: A 389 GLU cc_start: 0.5914 (OUTLIER) cc_final: 0.5603 (tt0) REVERT: B 46 GLU cc_start: 0.6739 (tt0) cc_final: 0.6489 (mt-10) REVERT: B 155 MET cc_start: 0.7332 (tpp) cc_final: 0.7119 (tpp) REVERT: B 225 SER cc_start: 0.7001 (t) cc_final: 0.6631 (p) REVERT: C 24 ASP cc_start: 0.7947 (m-30) cc_final: 0.7516 (m-30) REVERT: C 138 MET cc_start: 0.7025 (tpt) cc_final: 0.6802 (tpt) REVERT: C 168 LYS cc_start: 0.6976 (mptt) cc_final: 0.6599 (mmmt) REVERT: C 181 LYS cc_start: 0.8046 (ttpp) cc_final: 0.7563 (mtpt) REVERT: C 204 SER cc_start: 0.8282 (OUTLIER) cc_final: 0.7803 (m) REVERT: C 371 ILE cc_start: 0.8097 (tp) cc_final: 0.7807 (tp) REVERT: D 8 HIS cc_start: 0.7138 (m-70) cc_final: 0.6897 (m90) REVERT: D 264 GLU cc_start: 0.7370 (mm-30) cc_final: 0.6968 (mt-10) REVERT: D 298 LYS cc_start: 0.6892 (mmtt) cc_final: 0.6626 (mtmt) REVERT: D 406 SER cc_start: 0.7882 (t) cc_final: 0.7384 (p) REVERT: D 419 MET cc_start: 0.7103 (mmt) cc_final: 0.6792 (mmt) REVERT: E 155 MET cc_start: 0.4520 (tpp) cc_final: 0.4289 (tpt) REVERT: E 158 TYR cc_start: 0.5476 (p90) cc_final: 0.5053 (p90) REVERT: E 228 MET cc_start: 0.7585 (mtm) cc_final: 0.7265 (mtt) REVERT: E 371 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7139 (tp) REVERT: F 3 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6561 (tt0) REVERT: F 47 TYR cc_start: 0.7924 (m-80) cc_final: 0.7673 (m-80) REVERT: F 90 LEU cc_start: 0.5471 (OUTLIER) cc_final: 0.5128 (mm) REVERT: F 155 MET cc_start: 0.5860 (OUTLIER) cc_final: 0.5520 (ptt) REVERT: F 307 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8355 (mp) REVERT: F 326 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7567 (mp0) outliers start: 82 outliers final: 32 residues processed: 402 average time/residue: 0.1240 time to fit residues: 79.2034 Evaluate side-chains 312 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 273 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 423 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 145 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 237 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 250 optimal weight: 0.2980 chunk 168 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 ASN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN C 125 ASN D 200 ASN E 399 GLN E 426 GLN F 398 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.210985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.196270 restraints weight = 20989.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.190853 restraints weight = 29313.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.185393 restraints weight = 19752.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.185757 restraints weight = 24108.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.186507 restraints weight = 19250.179| |-----------------------------------------------------------------------------| r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21368 Z= 0.131 Angle : 0.588 9.865 28966 Z= 0.309 Chirality : 0.043 0.279 3246 Planarity : 0.003 0.036 3599 Dihedral : 10.202 167.457 2946 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.23 % Allowed : 16.31 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.17), residues: 2580 helix: 1.04 (0.14), residues: 1339 sheet: -1.36 (0.28), residues: 353 loop : -1.44 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 340 TYR 0.027 0.001 TYR D 15 PHE 0.016 0.002 PHE E 11 TRP 0.020 0.002 TRP E 20 HIS 0.004 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (21368) covalent geometry : angle 0.58805 / 0.31 (28966) hydrogen bonds : bond 0.03312 / 2.21 ( 1054) hydrogen bonds : angle 4.77297 / 3.36 ( 3030) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 298 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 LYS cc_start: 0.5839 (OUTLIER) cc_final: 0.5252 (ttpt) REVERT: B 74 LYS cc_start: 0.7715 (tppt) cc_final: 0.7502 (tptp) REVERT: B 138 MET cc_start: 0.7530 (mmm) cc_final: 0.6814 (mmm) REVERT: B 225 SER cc_start: 0.6906 (t) cc_final: 0.6683 (p) REVERT: C 24 ASP cc_start: 0.7880 (m-30) cc_final: 0.7395 (m-30) REVERT: C 168 LYS cc_start: 0.6903 (mptt) cc_final: 0.6506 (mmmt) REVERT: C 181 LYS cc_start: 0.8016 (ttpp) cc_final: 0.7544 (mtpt) REVERT: C 226 MET cc_start: 0.7944 (mmp) cc_final: 0.7672 (mmp) REVERT: D 8 HIS cc_start: 0.7050 (m-70) cc_final: 0.6824 (m90) REVERT: D 23 MET cc_start: 0.8171 (tpp) cc_final: 0.7860 (tpp) REVERT: D 264 GLU cc_start: 0.7284 (mm-30) cc_final: 0.7053 (mt-10) REVERT: D 406 SER cc_start: 0.7819 (t) cc_final: 0.7317 (p) REVERT: D 419 MET cc_start: 0.7163 (mmt) cc_final: 0.6877 (mmt) REVERT: E 155 MET cc_start: 0.4388 (tpp) cc_final: 0.4088 (tpt) REVERT: E 158 TYR cc_start: 0.5535 (p90) cc_final: 0.5172 (p90) REVERT: E 228 MET cc_start: 0.7564 (mtm) cc_final: 0.7335 (mtt) REVERT: E 371 ILE cc_start: 0.7607 (OUTLIER) cc_final: 0.7071 (tp) REVERT: F 3 GLU cc_start: 0.7295 (mm-30) cc_final: 0.7084 (mm-30) REVERT: F 90 LEU cc_start: 0.5137 (OUTLIER) cc_final: 0.4901 (mm) REVERT: F 112 GLU cc_start: 0.6279 (OUTLIER) cc_final: 0.6044 (mp0) REVERT: F 155 MET cc_start: 0.5814 (OUTLIER) cc_final: 0.5512 (ptt) REVERT: F 307 ILE cc_start: 0.8599 (mm) cc_final: 0.8317 (mp) REVERT: F 326 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7647 (mp0) outliers start: 50 outliers final: 22 residues processed: 334 average time/residue: 0.1315 time to fit residues: 70.4204 Evaluate side-chains 305 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 278 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 155 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 2 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 175 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 188 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 45 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN E 399 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.204931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.190524 restraints weight = 20972.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.184307 restraints weight = 28648.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.180659 restraints weight = 19789.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.181024 restraints weight = 19086.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.181598 restraints weight = 16494.423| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.5707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21368 Z= 0.161 Angle : 0.596 13.130 28966 Z= 0.314 Chirality : 0.043 0.217 3246 Planarity : 0.003 0.038 3599 Dihedral : 10.297 168.568 2946 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.82 % Allowed : 16.76 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.26 (0.17), residues: 2580 helix: 1.06 (0.15), residues: 1340 sheet: -1.51 (0.27), residues: 351 loop : -1.45 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 340 TYR 0.023 0.002 TYR B 312 PHE 0.021 0.002 PHE E 11 TRP 0.024 0.002 TRP E 20 HIS 0.004 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (21368) covalent geometry : angle 0.59621 / 0.31 (28966) hydrogen bonds : bond 0.03352 / 2.25 ( 1054) hydrogen bonds : angle 4.75360 / 3.36 ( 3030) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 306 time to evaluate : 0.699 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: A 57 ASN cc_start: 0.6556 (m-40) cc_final: 0.6077 (m110) REVERT: A 333 LYS cc_start: 0.6017 (OUTLIER) cc_final: 0.5279 (ttpt) REVERT: A 389 GLU cc_start: 0.5916 (OUTLIER) cc_final: 0.5479 (tt0) REVERT: B 138 MET cc_start: 0.7780 (mmm) cc_final: 0.7219 (mmm) REVERT: C 24 ASP cc_start: 0.7942 (m-30) cc_final: 0.7492 (m-30) REVERT: C 181 LYS cc_start: 0.8097 (ttpp) cc_final: 0.7580 (mtpt) REVERT: D 1 MET cc_start: 0.7367 (ppp) cc_final: 0.7082 (ppp) REVERT: D 154 TRP cc_start: 0.7724 (t60) cc_final: 0.7359 (t60) REVERT: D 264 GLU cc_start: 0.7293 (mm-30) cc_final: 0.7034 (mt-10) REVERT: D 298 LYS cc_start: 0.6887 (mmtt) cc_final: 0.6522 (mtmt) REVERT: D 338 GLU cc_start: 0.8193 (tp30) cc_final: 0.7228 (mt-10) REVERT: D 419 MET cc_start: 0.7148 (mmt) cc_final: 0.6832 (mmt) REVERT: E 155 MET cc_start: 0.4724 (tpp) cc_final: 0.4484 (tpt) REVERT: E 158 TYR cc_start: 0.5539 (p90) cc_final: 0.5246 (p90) REVERT: E 228 MET cc_start: 0.7558 (mtm) cc_final: 0.7301 (mtt) REVERT: E 276 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7396 (mm) REVERT: E 371 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7282 (tp) REVERT: F 155 MET cc_start: 0.5857 (OUTLIER) cc_final: 0.5555 (ptt) REVERT: F 307 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8219 (mp) outliers start: 63 outliers final: 30 residues processed: 350 average time/residue: 0.1296 time to fit residues: 72.2037 Evaluate side-chains 313 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 277 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 404 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 243 optimal weight: 5.9990 chunk 166 optimal weight: 0.6980 chunk 175 optimal weight: 6.9990 chunk 226 optimal weight: 1.9990 chunk 177 optimal weight: 8.9990 chunk 227 optimal weight: 5.9990 chunk 174 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 123 optimal weight: 0.0570 chunk 65 optimal weight: 1.9990 overall best weight: 1.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 ASN A 355 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN D 200 ASN D 422 GLN E 399 GLN ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.203218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.185132 restraints weight = 21214.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.183594 restraints weight = 29823.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.184822 restraints weight = 27774.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.184790 restraints weight = 18397.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.184944 restraints weight = 18908.376| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.6114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21368 Z= 0.150 Angle : 0.595 13.737 28966 Z= 0.311 Chirality : 0.043 0.254 3246 Planarity : 0.003 0.039 3599 Dihedral : 10.299 167.976 2946 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.82 % Allowed : 18.05 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.17), residues: 2580 helix: 1.08 (0.15), residues: 1339 sheet: -1.52 (0.28), residues: 351 loop : -1.43 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 340 TYR 0.021 0.001 TYR E 329 PHE 0.014 0.002 PHE E 417 TRP 0.024 0.002 TRP E 20 HIS 0.006 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (21368) covalent geometry : angle 0.59500 / 0.31 (28966) hydrogen bonds : bond 0.03202 / 2.14 ( 1054) hydrogen bonds : angle 4.72071 / 3.33 ( 3030) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 300 time to evaluate : 0.799 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: A 1 MET cc_start: 0.7580 (tpt) cc_final: 0.6897 (tpt) REVERT: A 107 THR cc_start: 0.6986 (OUTLIER) cc_final: 0.6674 (m) REVERT: A 165 TYR cc_start: 0.7236 (m-10) cc_final: 0.6592 (m-10) REVERT: A 333 LYS cc_start: 0.5960 (OUTLIER) cc_final: 0.5322 (ttpt) REVERT: A 389 GLU cc_start: 0.5474 (OUTLIER) cc_final: 0.5188 (tt0) REVERT: B 138 MET cc_start: 0.7742 (mmm) cc_final: 0.7258 (mmm) REVERT: C 24 ASP cc_start: 0.7830 (m-30) cc_final: 0.7425 (m-30) REVERT: C 181 LYS cc_start: 0.8043 (ttpp) cc_final: 0.7534 (mtpt) REVERT: C 384 MET cc_start: 0.7822 (ttm) cc_final: 0.7352 (mtp) REVERT: D 1 MET cc_start: 0.7451 (ppp) cc_final: 0.7211 (ppp) REVERT: D 154 TRP cc_start: 0.7551 (t60) cc_final: 0.7315 (t60) REVERT: D 155 MET cc_start: 0.8375 (mmm) cc_final: 0.8100 (tpp) REVERT: D 264 GLU cc_start: 0.7248 (mm-30) cc_final: 0.7039 (mt-10) REVERT: D 419 MET cc_start: 0.7182 (mmt) cc_final: 0.6886 (mmt) REVERT: E 23 MET cc_start: 0.7295 (mmp) cc_final: 0.6840 (mmp) REVERT: E 158 TYR cc_start: 0.5605 (p90) cc_final: 0.5356 (p90) REVERT: E 228 MET cc_start: 0.7619 (mtm) cc_final: 0.7373 (mtt) REVERT: E 276 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7722 (mm) REVERT: E 371 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7344 (tp) REVERT: E 385 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6847 (tt) REVERT: F 112 GLU cc_start: 0.6237 (mp0) cc_final: 0.6018 (mp0) REVERT: F 307 ILE cc_start: 0.8572 (mm) cc_final: 0.8335 (mp) REVERT: F 392 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.5954 (pt0) outliers start: 63 outliers final: 33 residues processed: 348 average time/residue: 0.1295 time to fit residues: 71.4980 Evaluate side-chains 318 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 278 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 392 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 221 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 99 optimal weight: 0.1980 chunk 62 optimal weight: 0.7980 chunk 6 optimal weight: 20.0000 chunk 133 optimal weight: 8.9990 chunk 143 optimal weight: 9.9990 chunk 227 optimal weight: 0.0470 chunk 243 optimal weight: 5.9990 chunk 253 optimal weight: 2.9990 chunk 223 optimal weight: 20.0000 overall best weight: 1.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.204036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.184726 restraints weight = 21204.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.184231 restraints weight = 31967.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.185055 restraints weight = 27188.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.183616 restraints weight = 21730.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.184152 restraints weight = 20227.227| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.6341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21368 Z= 0.131 Angle : 0.587 14.296 28966 Z= 0.306 Chirality : 0.042 0.214 3246 Planarity : 0.003 0.041 3599 Dihedral : 10.216 165.849 2944 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.59 % Allowed : 18.19 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.17), residues: 2580 helix: 1.17 (0.15), residues: 1343 sheet: -1.50 (0.28), residues: 354 loop : -1.46 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 177 TYR 0.020 0.001 TYR F 15 PHE 0.017 0.002 PHE A 11 TRP 0.020 0.001 TRP E 20 HIS 0.004 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (21368) covalent geometry : angle 0.58715 / 0.31 (28966) hydrogen bonds : bond 0.03084 / 2.08 ( 1054) hydrogen bonds : angle 4.64167 / 3.27 ( 3030) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 283 time to evaluate : 0.784 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 107 THR cc_start: 0.6945 (OUTLIER) cc_final: 0.6628 (m) REVERT: A 145 SER cc_start: 0.8171 (m) cc_final: 0.7964 (p) REVERT: A 165 TYR cc_start: 0.7366 (m-10) cc_final: 0.6639 (m-10) REVERT: A 196 MET cc_start: 0.7369 (mtt) cc_final: 0.7165 (mmm) REVERT: A 333 LYS cc_start: 0.5929 (OUTLIER) cc_final: 0.5251 (ttpt) REVERT: A 389 GLU cc_start: 0.5475 (OUTLIER) cc_final: 0.5175 (tt0) REVERT: B 138 MET cc_start: 0.7626 (mmm) cc_final: 0.7273 (mmm) REVERT: C 24 ASP cc_start: 0.7799 (m-30) cc_final: 0.7421 (m-30) REVERT: C 138 MET cc_start: 0.7177 (tpt) cc_final: 0.6879 (tpt) REVERT: C 145 SER cc_start: 0.8722 (p) cc_final: 0.8169 (m) REVERT: C 181 LYS cc_start: 0.8075 (ttpp) cc_final: 0.7591 (mtpt) REVERT: D 23 MET cc_start: 0.8026 (tpp) cc_final: 0.7779 (mmt) REVERT: D 154 TRP cc_start: 0.7607 (t60) cc_final: 0.7292 (t60) REVERT: D 155 MET cc_start: 0.8422 (mmm) cc_final: 0.8112 (tpp) REVERT: D 264 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7067 (mt-10) REVERT: D 338 GLU cc_start: 0.8199 (tp30) cc_final: 0.7221 (mt-10) REVERT: D 419 MET cc_start: 0.7164 (mmt) cc_final: 0.6884 (mmt) REVERT: E 23 MET cc_start: 0.7287 (mmp) cc_final: 0.6924 (mmp) REVERT: E 158 TYR cc_start: 0.5583 (p90) cc_final: 0.5372 (p90) REVERT: E 361 TRP cc_start: 0.7582 (OUTLIER) cc_final: 0.7253 (m-10) REVERT: F 112 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.6143 (mp0) REVERT: F 307 ILE cc_start: 0.8576 (mm) cc_final: 0.8311 (mp) outliers start: 58 outliers final: 34 residues processed: 325 average time/residue: 0.1249 time to fit residues: 66.4342 Evaluate side-chains 308 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 269 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 361 TRP Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 112 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 142 optimal weight: 0.8980 chunk 209 optimal weight: 0.9980 chunk 238 optimal weight: 6.9990 chunk 253 optimal weight: 6.9990 chunk 166 optimal weight: 0.4980 chunk 40 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 191 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 HIS ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.202608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.186788 restraints weight = 21087.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.186403 restraints weight = 32587.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.186744 restraints weight = 30107.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.186950 restraints weight = 23734.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.187085 restraints weight = 20136.446| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.6580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21368 Z= 0.132 Angle : 0.587 14.580 28966 Z= 0.306 Chirality : 0.042 0.213 3246 Planarity : 0.003 0.044 3599 Dihedral : 10.217 164.420 2944 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.41 % Allowed : 18.86 % Favored : 78.73 % 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 (0.17), residues: 2580 helix: 1.22 (0.15), residues: 1342 sheet: -1.49 (0.28), residues: 354 loop : -1.47 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 340 TYR 0.018 0.001 TYR A 47 PHE 0.019 0.002 PHE A 11 TRP 0.037 0.002 TRP E 428 HIS 0.004 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (21368) covalent geometry : angle 0.58680 / 0.31 (28966) hydrogen bonds : bond 0.03044 / 2.04 ( 1054) hydrogen bonds : angle 4.63611 / 3.27 ( 3030) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 278 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.5477 (m-40) cc_final: 0.4998 (m-40) REVERT: A 107 THR cc_start: 0.6922 (OUTLIER) cc_final: 0.6589 (m) REVERT: A 165 TYR cc_start: 0.7279 (m-10) cc_final: 0.6685 (m-10) REVERT: A 170 ARG cc_start: 0.7938 (mtp-110) cc_final: 0.7703 (mtp-110) REVERT: A 333 LYS cc_start: 0.5991 (OUTLIER) cc_final: 0.5365 (ttpt) REVERT: B 74 LYS cc_start: 0.7894 (tptp) cc_final: 0.7312 (tppt) REVERT: C 24 ASP cc_start: 0.7751 (m-30) cc_final: 0.7527 (m-30) REVERT: C 138 MET cc_start: 0.7175 (tpt) cc_final: 0.6852 (tpt) REVERT: C 145 SER cc_start: 0.8642 (p) cc_final: 0.8113 (m) REVERT: C 181 LYS cc_start: 0.8135 (ttpp) cc_final: 0.7585 (mtpt) REVERT: D 23 MET cc_start: 0.7861 (tpp) cc_final: 0.7625 (mmt) REVERT: D 154 TRP cc_start: 0.7601 (t60) cc_final: 0.7306 (t60) REVERT: D 155 MET cc_start: 0.8330 (mmm) cc_final: 0.8013 (tpp) REVERT: D 338 GLU cc_start: 0.8245 (tp30) cc_final: 0.7336 (mt-10) REVERT: D 419 MET cc_start: 0.7187 (mmt) cc_final: 0.6924 (mmt) REVERT: E 11 PHE cc_start: 0.7272 (m-80) cc_final: 0.7028 (m-80) REVERT: E 23 MET cc_start: 0.7307 (mmp) cc_final: 0.6968 (mmt) REVERT: E 361 TRP cc_start: 0.7573 (OUTLIER) cc_final: 0.7216 (m-10) REVERT: E 371 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7347 (tp) REVERT: F 307 ILE cc_start: 0.8572 (mm) cc_final: 0.8318 (mp) REVERT: F 428 TRP cc_start: 0.6943 (m-10) cc_final: 0.6686 (m-10) outliers start: 54 outliers final: 35 residues processed: 318 average time/residue: 0.1265 time to fit residues: 65.6475 Evaluate side-chains 306 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 267 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 361 TRP Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 0.6980 chunk 194 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 217 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 131 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.198465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.180791 restraints weight = 21237.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.179642 restraints weight = 29853.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.180380 restraints weight = 27014.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.179422 restraints weight = 24234.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.180017 restraints weight = 20410.504| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.6926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21368 Z= 0.151 Angle : 0.617 14.600 28966 Z= 0.321 Chirality : 0.043 0.218 3246 Planarity : 0.003 0.045 3599 Dihedral : 10.306 165.109 2944 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.50 % Allowed : 19.03 % Favored : 78.46 % 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: -0.21 (0.17), residues: 2580 helix: 1.19 (0.15), residues: 1334 sheet: -1.54 (0.28), residues: 354 loop : -1.53 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 340 TYR 0.048 0.002 TYR F 165 PHE 0.028 0.002 PHE C 28 TRP 0.027 0.002 TRP E 428 HIS 0.005 0.001 HIS E 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (21368) covalent geometry : angle 0.61673 / 0.32 (28966) hydrogen bonds : bond 0.03143 / 2.10 ( 1054) hydrogen bonds : angle 4.69591 / 3.32 ( 3030) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 282 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.5629 (m-40) cc_final: 0.5236 (m-40) REVERT: A 165 TYR cc_start: 0.7392 (m-10) cc_final: 0.6722 (m-10) REVERT: A 333 LYS cc_start: 0.6120 (OUTLIER) cc_final: 0.5441 (ttpt) REVERT: B 118 GLU cc_start: 0.7023 (tt0) cc_final: 0.6344 (mt-10) REVERT: C 24 ASP cc_start: 0.7727 (m-30) cc_final: 0.7395 (m-30) REVERT: C 92 LYS cc_start: 0.7576 (mmmm) cc_final: 0.7188 (tptt) REVERT: C 138 MET cc_start: 0.7510 (tpt) cc_final: 0.7231 (tpt) REVERT: C 145 SER cc_start: 0.8702 (p) cc_final: 0.8178 (m) REVERT: C 181 LYS cc_start: 0.8043 (ttpp) cc_final: 0.7603 (mtpt) REVERT: D 1 MET cc_start: 0.7443 (ppp) cc_final: 0.7150 (ppp) REVERT: D 154 TRP cc_start: 0.7686 (t60) cc_final: 0.7329 (t60) REVERT: D 155 MET cc_start: 0.8499 (mmm) cc_final: 0.8248 (tpp) REVERT: D 338 GLU cc_start: 0.8173 (tp30) cc_final: 0.7246 (mt-10) REVERT: E 11 PHE cc_start: 0.7289 (m-80) cc_final: 0.7069 (m-80) REVERT: E 23 MET cc_start: 0.7473 (mmp) cc_final: 0.7187 (mmt) REVERT: E 361 TRP cc_start: 0.7565 (OUTLIER) cc_final: 0.7172 (m-10) REVERT: E 371 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7402 (tp) REVERT: F 90 LEU cc_start: 0.5259 (OUTLIER) cc_final: 0.4967 (mm) REVERT: F 112 GLU cc_start: 0.6167 (mp0) cc_final: 0.5909 (mp0) REVERT: F 263 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6500 (mmt) REVERT: F 428 TRP cc_start: 0.6873 (m-10) cc_final: 0.6542 (m-10) outliers start: 56 outliers final: 37 residues processed: 322 average time/residue: 0.1248 time to fit residues: 65.4845 Evaluate side-chains 315 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 273 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 361 TRP Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 263 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 0.0020 chunk 40 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 139 optimal weight: 0.0370 chunk 34 optimal weight: 9.9990 overall best weight: 0.6072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN E 253 HIS F 398 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.202366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.183945 restraints weight = 21180.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.183882 restraints weight = 30830.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.184877 restraints weight = 26893.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.184107 restraints weight = 21189.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.186044 restraints weight = 17609.797| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.6991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21368 Z= 0.118 Angle : 0.603 15.292 28966 Z= 0.310 Chirality : 0.042 0.295 3246 Planarity : 0.003 0.045 3599 Dihedral : 10.214 164.369 2944 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.65 % Allowed : 19.93 % Favored : 78.42 % 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 (0.17), residues: 2580 helix: 1.31 (0.15), residues: 1333 sheet: -1.45 (0.28), residues: 346 loop : -1.53 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 340 TYR 0.021 0.001 TYR F 70 PHE 0.021 0.002 PHE C 28 TRP 0.028 0.001 TRP E 428 HIS 0.019 0.001 HIS E 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (21368) covalent geometry : angle 0.60305 / 0.31 (28966) hydrogen bonds : bond 0.02948 / 1.97 ( 1054) hydrogen bonds : angle 4.60666 / 3.25 ( 3030) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 274 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.5938 (m-40) cc_final: 0.5527 (m-40) REVERT: A 165 TYR cc_start: 0.7329 (m-10) cc_final: 0.6704 (m-10) REVERT: A 333 LYS cc_start: 0.5954 (OUTLIER) cc_final: 0.5268 (ttpt) REVERT: A 398 GLN cc_start: 0.5923 (pm20) cc_final: 0.5680 (pm20) REVERT: B 118 GLU cc_start: 0.6916 (tt0) cc_final: 0.6185 (mt-10) REVERT: B 166 MET cc_start: 0.7121 (tpp) cc_final: 0.6743 (mmt) REVERT: C 24 ASP cc_start: 0.7746 (m-30) cc_final: 0.7429 (m-30) REVERT: C 138 MET cc_start: 0.7532 (tpt) cc_final: 0.7227 (tpt) REVERT: C 145 SER cc_start: 0.8698 (p) cc_final: 0.8177 (m) REVERT: C 181 LYS cc_start: 0.8046 (ttpp) cc_final: 0.7600 (mtpt) REVERT: D 154 TRP cc_start: 0.7723 (t60) cc_final: 0.7366 (t60) REVERT: D 155 MET cc_start: 0.8477 (mmm) cc_final: 0.8242 (tpp) REVERT: D 338 GLU cc_start: 0.8094 (tp30) cc_final: 0.7198 (mt-10) REVERT: E 11 PHE cc_start: 0.7316 (m-80) cc_final: 0.7094 (m-80) REVERT: E 23 MET cc_start: 0.7481 (mmp) cc_final: 0.7180 (mmt) REVERT: E 361 TRP cc_start: 0.7482 (OUTLIER) cc_final: 0.7060 (m-10) REVERT: E 371 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7163 (tp) REVERT: F 112 GLU cc_start: 0.6069 (mp0) cc_final: 0.5833 (mp0) REVERT: F 263 MET cc_start: 0.6963 (OUTLIER) cc_final: 0.6488 (mmt) REVERT: F 428 TRP cc_start: 0.6732 (m-10) cc_final: 0.6478 (m-10) outliers start: 37 outliers final: 25 residues processed: 299 average time/residue: 0.1206 time to fit residues: 58.5831 Evaluate side-chains 292 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 263 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 361 TRP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 263 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 29 optimal weight: 2.9990 chunk 214 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 184 optimal weight: 0.0370 chunk 33 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 238 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 216 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.203235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.183329 restraints weight = 21122.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.182484 restraints weight = 32604.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.184012 restraints weight = 26937.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.183552 restraints weight = 17472.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.185110 restraints weight = 15804.456| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.7091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21368 Z= 0.120 Angle : 0.608 15.013 28966 Z= 0.311 Chirality : 0.042 0.213 3246 Planarity : 0.003 0.044 3599 Dihedral : 10.184 164.880 2944 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.47 % Allowed : 20.29 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.17), residues: 2580 helix: 1.36 (0.15), residues: 1337 sheet: -1.46 (0.28), residues: 358 loop : -1.49 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 340 TYR 0.018 0.001 TYR A 47 PHE 0.019 0.002 PHE C 16 TRP 0.023 0.001 TRP E 428 HIS 0.006 0.001 HIS E 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (21368) covalent geometry : angle 0.60827 / 0.31 (28966) hydrogen bonds : bond 0.02908 / 1.95 ( 1054) hydrogen bonds : angle 4.55705 / 3.22 ( 3030) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3052.49 seconds wall clock time: 54 minutes 3.44 seconds (3243.44 seconds total)