Starting phenix.real_space_refine on Fri Aug 7 09:06:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g0z_29658/08_2026/8g0z_29658.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g0z_29658/08_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_29658/08_2026/8g0z_29658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g0z_29658/08_2026/8g0z_29658.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8g0z_29658/08_2026/8g0z_29658.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g0z_29658/08_2026/8g0z_29658.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g0z_29658/08_2026/8g0z_29658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g0z_29658/08_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-2.2rc3-6140/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: 4.45, per 1000 atoms: 0.21 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: 1.66 Conformation dependent library (CDL) restraints added in 955.2 milliseconds 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: 0.53 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: 3.83 Time building geometry restraints manager: 2.23 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.140 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.060 ------------------------------------------------------------------------------- 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 0.74911 / 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 : 0.739 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: 0.1559 time to fit residues: 114.2414 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 : 0.774 ------------------------------------------------------------------------------- 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 = 0.4496 r_free = 0.4496 target = 0.232682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.222330 restraints weight = 21066.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.213468 restraints weight = 25266.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.209820 restraints weight = 32093.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.211134 restraints weight = 24655.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.211009 restraints weight = 20639.616| |-----------------------------------------------------------------------------| r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 21368 Z= 0.216 Angle : 0.708 9.195 28966 Z= 0.377 Chirality : 0.047 0.254 3246 Planarity : 0.005 0.041 3599 Dihedral : 10.385 172.241 2956 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.31 % Allowed : 11.17 % 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: -0.29 (0.17), residues: 2580 helix: 0.82 (0.14), residues: 1341 sheet: -0.83 (0.28), residues: 345 loop : -1.42 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 236 TYR 0.035 0.002 TYR C 223 PHE 0.029 0.003 PHE E 11 TRP 0.019 0.002 TRP E 266 HIS 0.007 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 (21368) covalent geometry : angle 0.70844 / 0.38 (28966) hydrogen bonds : bond 0.04158 / 2.75 ( 1054) hydrogen bonds : angle 5.15807 / 3.65 ( 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 392 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 318 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 LYS cc_start: 0.5909 (OUTLIER) cc_final: 0.5266 (ttpt) REVERT: B 8 HIS cc_start: 0.7083 (m90) cc_final: 0.6881 (m-70) REVERT: C 168 LYS cc_start: 0.6672 (mptt) cc_final: 0.6451 (mmmt) REVERT: C 204 SER cc_start: 0.8096 (OUTLIER) cc_final: 0.7691 (m) REVERT: D 23 MET cc_start: 0.7970 (mmm) cc_final: 0.7731 (mmt) REVERT: D 43 HIS cc_start: 0.7294 (t-90) cc_final: 0.7029 (t-90) REVERT: E 80 LEU cc_start: 0.5220 (OUTLIER) cc_final: 0.4999 (mt) REVERT: E 158 TYR cc_start: 0.5412 (p90) cc_final: 0.4974 (p90) REVERT: E 228 MET cc_start: 0.7414 (mtm) cc_final: 0.7212 (mtt) REVERT: F 3 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6495 (mm-30) REVERT: F 112 GLU cc_start: 0.5998 (OUTLIER) cc_final: 0.5708 (mp0) REVERT: F 155 MET cc_start: 0.5811 (ptt) cc_final: 0.5343 (ptt) REVERT: F 165 TYR cc_start: 0.6914 (m-10) cc_final: 0.6116 (m-10) REVERT: F 280 TYR cc_start: 0.6076 (OUTLIER) cc_final: 0.4574 (t80) REVERT: F 418 LEU cc_start: 0.6258 (OUTLIER) cc_final: 0.6019 (mp) outliers start: 74 outliers final: 36 residues processed: 372 average time/residue: 0.1383 time to fit residues: 82.7243 Evaluate side-chains 297 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 255 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 226 MET 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 137 ILE 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 145 SER 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: 0.0270 chunk 134 optimal weight: 0.7980 chunk 129 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 252 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 176 optimal weight: 5.9990 chunk 258 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN D 200 ASN E 355 GLN F 398 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.226070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.206306 restraints weight = 20923.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.204917 restraints weight = 29360.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.206869 restraints weight = 25623.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.206567 restraints weight = 17192.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.206858 restraints weight = 15588.955| |-----------------------------------------------------------------------------| r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 21368 Z= 0.143 Angle : 0.573 7.751 28966 Z= 0.304 Chirality : 0.043 0.230 3246 Planarity : 0.004 0.040 3599 Dihedral : 10.059 170.460 2950 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.46 % Allowed : 13.27 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.17), residues: 2580 helix: 1.12 (0.14), residues: 1341 sheet: -0.90 (0.29), residues: 343 loop : -1.38 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 236 TYR 0.017 0.002 TYR E 47 PHE 0.017 0.002 PHE E 11 TRP 0.021 0.002 TRP F 428 HIS 0.008 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (21368) covalent geometry : angle 0.57252 / 0.30 (28966) hydrogen bonds : bond 0.03679 / 2.48 ( 1054) hydrogen bonds : angle 4.80605 / 3.39 ( 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 335 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 280 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 LYS cc_start: 0.5961 (OUTLIER) cc_final: 0.5365 (ttpt) REVERT: B 8 HIS cc_start: 0.7090 (m90) cc_final: 0.6865 (m-70) REVERT: B 43 HIS cc_start: 0.8052 (t-90) cc_final: 0.7630 (t-90) REVERT: B 46 GLU cc_start: 0.6332 (tt0) cc_final: 0.6033 (mt-10) REVERT: B 138 MET cc_start: 0.6854 (mmm) cc_final: 0.6607 (mmm) REVERT: B 225 SER cc_start: 0.6639 (t) cc_final: 0.6328 (p) REVERT: C 24 ASP cc_start: 0.7808 (m-30) cc_final: 0.7315 (m-30) REVERT: C 168 LYS cc_start: 0.6640 (mptt) cc_final: 0.6404 (mmmt) REVERT: C 226 MET cc_start: 0.8076 (mmp) cc_final: 0.7857 (mmp) REVERT: D 23 MET cc_start: 0.7956 (mmm) cc_final: 0.7577 (mmt) REVERT: D 43 HIS cc_start: 0.7300 (t-90) cc_final: 0.7048 (t-90) REVERT: E 137 ILE cc_start: 0.8578 (mt) cc_final: 0.8314 (tt) REVERT: E 152 HIS cc_start: 0.7017 (OUTLIER) cc_final: 0.6783 (m-70) REVERT: E 158 TYR cc_start: 0.5554 (p90) cc_final: 0.5041 (p90) REVERT: E 228 MET cc_start: 0.7380 (mtm) cc_final: 0.7115 (mtt) REVERT: E 272 LEU cc_start: 0.8120 (tp) cc_final: 0.7737 (tp) REVERT: F 3 GLU cc_start: 0.6892 (mm-30) cc_final: 0.6397 (tm-30) REVERT: F 47 TYR cc_start: 0.7509 (m-80) cc_final: 0.7293 (m-80) REVERT: F 90 LEU cc_start: 0.5281 (OUTLIER) cc_final: 0.4980 (mm) REVERT: F 165 TYR cc_start: 0.7028 (m-10) cc_final: 0.6090 (m-10) outliers start: 55 outliers final: 27 residues processed: 323 average time/residue: 0.1364 time to fit residues: 71.4597 Evaluate side-chains 273 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 243 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 174 PHE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 152 HIS 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 364 SER 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 99 GLN Chi-restraints excluded: chain F residue 140 GLN 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: 0.2980 chunk 67 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 237 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 201 optimal weight: 3.9990 chunk 219 optimal weight: 0.9980 chunk 250 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN C 200 ASN D 200 ASN ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 399 GLN F 398 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.214311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.195594 restraints weight = 21022.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.194960 restraints weight = 30976.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.195981 restraints weight = 25907.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.195333 restraints weight = 18753.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.195744 restraints weight = 17745.680| |-----------------------------------------------------------------------------| r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21368 Z= 0.169 Angle : 0.602 8.192 28966 Z= 0.319 Chirality : 0.044 0.237 3246 Planarity : 0.004 0.046 3599 Dihedral : 10.167 171.058 2946 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.64 % Allowed : 14.75 % Favored : 82.62 % 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: -0.19 (0.17), residues: 2580 helix: 1.05 (0.14), residues: 1341 sheet: -1.12 (0.28), residues: 337 loop : -1.48 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 340 TYR 0.026 0.002 TYR F 15 PHE 0.019 0.002 PHE E 11 TRP 0.019 0.002 TRP F 428 HIS 0.005 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (21368) covalent geometry : angle 0.60246 / 0.32 (28966) hydrogen bonds : bond 0.03468 / 2.32 ( 1054) hydrogen bonds : angle 4.80750 / 3.38 ( 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 367 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 308 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 LYS cc_start: 0.5960 (OUTLIER) cc_final: 0.5448 (ttpt) REVERT: A 389 GLU cc_start: 0.5446 (OUTLIER) cc_final: 0.5184 (tt0) REVERT: B 138 MET cc_start: 0.7504 (mmm) cc_final: 0.6651 (mmm) REVERT: B 225 SER cc_start: 0.6861 (t) cc_final: 0.6567 (p) REVERT: C 24 ASP cc_start: 0.7856 (m-30) cc_final: 0.7344 (m-30) REVERT: C 168 LYS cc_start: 0.6820 (mptt) cc_final: 0.6512 (mmmt) REVERT: C 181 LYS cc_start: 0.7958 (ttpp) cc_final: 0.7431 (mtpt) REVERT: C 226 MET cc_start: 0.8102 (mmp) cc_final: 0.7844 (mmp) REVERT: C 384 MET cc_start: 0.7436 (ttm) cc_final: 0.6978 (mtp) REVERT: D 406 SER cc_start: 0.7505 (t) cc_final: 0.6996 (p) REVERT: E 137 ILE cc_start: 0.8556 (mt) cc_final: 0.8270 (tt) REVERT: E 139 ARG cc_start: 0.6196 (ttm110) cc_final: 0.5929 (ttp-170) REVERT: E 158 TYR cc_start: 0.5510 (p90) cc_final: 0.5147 (p90) REVERT: E 371 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7230 (tp) REVERT: F 3 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6635 (tm-30) REVERT: F 90 LEU cc_start: 0.5437 (OUTLIER) cc_final: 0.5063 (mm) REVERT: F 112 GLU cc_start: 0.5959 (mp0) cc_final: 0.5735 (mp0) REVERT: F 307 ILE cc_start: 0.8598 (mm) cc_final: 0.8275 (mp) outliers start: 59 outliers final: 32 residues processed: 351 average time/residue: 0.1420 time to fit residues: 79.7394 Evaluate side-chains 306 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 270 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 174 PHE Chi-restraints excluded: chain A residue 255 SER 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 B residue 19 VAL Chi-restraints excluded: chain B residue 53 ILE 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 C residue 387 VAL Chi-restraints excluded: chain D residue 50 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 4 ILE Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 245 SER 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 E residue 429 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 404 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 2 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 157 optimal weight: 0.0770 chunk 175 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 188 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 overall best weight: 1.1340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 ASN A 240 ASN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN C 125 ASN D 8 HIS F 398 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.214239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.193803 restraints weight = 20758.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.192961 restraints weight = 32943.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.193917 restraints weight = 26895.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.194369 restraints weight = 20712.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.194436 restraints weight = 18747.191| |-----------------------------------------------------------------------------| r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.4999 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= 0.128 Angle : 0.573 15.579 28966 Z= 0.301 Chirality : 0.042 0.294 3246 Planarity : 0.003 0.039 3599 Dihedral : 10.064 166.465 2946 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.46 % Allowed : 16.26 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.17), residues: 2580 helix: 1.29 (0.15), residues: 1332 sheet: -1.18 (0.28), residues: 349 loop : -1.48 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 124 TYR 0.029 0.001 TYR D 15 PHE 0.016 0.002 PHE E 11 TRP 0.018 0.001 TRP D 89 HIS 0.006 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (21368) covalent geometry : angle 0.57280 / 0.30 (28966) hydrogen bonds : bond 0.03198 / 2.15 ( 1054) hydrogen bonds : angle 4.65919 / 3.29 ( 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 336 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 281 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7588 (tpt) cc_final: 0.7020 (tpt) REVERT: A 333 LYS cc_start: 0.5826 (OUTLIER) cc_final: 0.5306 (ttpt) REVERT: A 389 GLU cc_start: 0.5323 (OUTLIER) cc_final: 0.5096 (tt0) REVERT: B 138 MET cc_start: 0.7466 (mmm) cc_final: 0.6603 (mmm) REVERT: B 155 MET cc_start: 0.7590 (tpp) cc_final: 0.7234 (tpp) REVERT: B 225 SER cc_start: 0.6954 (t) cc_final: 0.6744 (p) REVERT: C 24 ASP cc_start: 0.7772 (m-30) cc_final: 0.7286 (m-30) REVERT: C 168 LYS cc_start: 0.6726 (mptt) cc_final: 0.6425 (mmmt) REVERT: C 181 LYS cc_start: 0.7917 (ttpp) cc_final: 0.7401 (mtpt) REVERT: C 226 MET cc_start: 0.7963 (mmp) cc_final: 0.7757 (mmp) REVERT: C 384 MET cc_start: 0.7621 (ttm) cc_final: 0.7204 (mtp) REVERT: D 237 ILE cc_start: 0.7840 (mm) cc_final: 0.7625 (mt) REVERT: D 264 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6887 (mt-10) REVERT: D 406 SER cc_start: 0.7547 (t) cc_final: 0.7002 (p) REVERT: E 20 TRP cc_start: 0.7166 (t-100) cc_final: 0.6939 (t-100) REVERT: E 138 MET cc_start: 0.8186 (tpt) cc_final: 0.7724 (tpt) REVERT: E 139 ARG cc_start: 0.6197 (ttm110) cc_final: 0.5924 (ttp-170) REVERT: E 158 TYR cc_start: 0.5515 (p90) cc_final: 0.5229 (p90) REVERT: E 371 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7158 (tp) REVERT: F 90 LEU cc_start: 0.5192 (OUTLIER) cc_final: 0.4983 (mm) REVERT: F 112 GLU cc_start: 0.6068 (OUTLIER) cc_final: 0.5850 (mp0) REVERT: F 307 ILE cc_start: 0.8662 (mm) cc_final: 0.8390 (mp) outliers start: 55 outliers final: 27 residues processed: 325 average time/residue: 0.1413 time to fit residues: 73.6255 Evaluate side-chains 293 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 261 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 255 SER 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 2 VAL 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 387 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 385 LEU 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 F residue 19 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 140 GLN Chi-restraints excluded: chain F residue 263 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 243 optimal weight: 0.4980 chunk 166 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 226 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 227 optimal weight: 8.9990 chunk 174 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 179 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 ASN A 355 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN C 295 ASN D 200 ASN ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 399 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.193898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.175442 restraints weight = 21536.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.173783 restraints weight = 33745.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.173932 restraints weight = 31150.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.173504 restraints weight = 25910.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.172652 restraints weight = 22668.132| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.6440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 21368 Z= 0.268 Angle : 0.755 10.877 28966 Z= 0.395 Chirality : 0.049 0.256 3246 Planarity : 0.005 0.058 3599 Dihedral : 10.745 174.670 2946 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.99 % Allowed : 17.11 % Favored : 79.89 % 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: -0.82 (0.16), residues: 2580 helix: 0.59 (0.14), residues: 1331 sheet: -1.67 (0.28), residues: 337 loop : -1.72 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 267 TYR 0.027 0.002 TYR C 223 PHE 0.026 0.003 PHE D 37 TRP 0.023 0.002 TRP B 162 HIS 0.005 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.27 (21368) covalent geometry : angle 0.75479 / 0.40 (28966) hydrogen bonds : bond 0.04023 / 2.71 ( 1054) hydrogen bonds : angle 5.11307 / 3.63 ( 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 407 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 340 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.6134 (m-40) cc_final: 0.5635 (m-40) REVERT: A 165 TYR cc_start: 0.7370 (m-10) cc_final: 0.6778 (m-10) REVERT: A 174 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.7061 (t80) REVERT: A 333 LYS cc_start: 0.6106 (OUTLIER) cc_final: 0.5304 (ttpt) REVERT: B 95 GLU cc_start: 0.7867 (tp30) cc_final: 0.7635 (tp30) REVERT: B 118 GLU cc_start: 0.7131 (tt0) cc_final: 0.6388 (mt-10) REVERT: B 196 MET cc_start: 0.6314 (mtm) cc_final: 0.5997 (ptp) REVERT: B 311 ASP cc_start: 0.7203 (t0) cc_final: 0.6897 (t0) REVERT: B 333 LYS cc_start: 0.6901 (ttpp) cc_final: 0.6604 (ttpp) REVERT: C 24 ASP cc_start: 0.8027 (m-30) cc_final: 0.7653 (m-30) REVERT: C 92 LYS cc_start: 0.7607 (mmmm) cc_final: 0.7188 (tptt) REVERT: C 145 SER cc_start: 0.8906 (p) cc_final: 0.8327 (m) REVERT: C 226 MET cc_start: 0.8176 (mmp) cc_final: 0.7948 (mmp) REVERT: C 385 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8279 (mt) REVERT: D 154 TRP cc_start: 0.7778 (t60) cc_final: 0.7425 (t60) REVERT: D 264 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7098 (mt-10) REVERT: D 298 LYS cc_start: 0.7213 (mmtt) cc_final: 0.6765 (mtmt) REVERT: E 20 TRP cc_start: 0.7535 (t-100) cc_final: 0.7239 (t-100) REVERT: E 23 MET cc_start: 0.7642 (mmp) cc_final: 0.7092 (mmt) REVERT: E 138 MET cc_start: 0.8616 (tpt) cc_final: 0.8141 (tpt) REVERT: E 158 TYR cc_start: 0.5629 (p90) cc_final: 0.5394 (p90) REVERT: E 272 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8202 (mp) REVERT: E 371 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7525 (tp) REVERT: F 90 LEU cc_start: 0.6053 (OUTLIER) cc_final: 0.5690 (mm) REVERT: F 112 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.6313 (mp0) outliers start: 67 outliers final: 32 residues processed: 384 average time/residue: 0.1427 time to fit residues: 87.1816 Evaluate side-chains 335 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 296 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 60 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 131 VAL 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 128 MET Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 272 LEU 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 53 ILE Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 307 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 221 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 99 optimal weight: 0.0040 chunk 62 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 chunk 133 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 227 optimal weight: 8.9990 chunk 243 optimal weight: 0.5980 chunk 253 optimal weight: 4.9990 chunk 223 optimal weight: 8.9990 overall best weight: 1.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 ASN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN D 216 GLN ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 399 GLN ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.197387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.179076 restraints weight = 21390.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.177776 restraints weight = 29812.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.179008 restraints weight = 28636.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.178583 restraints weight = 21125.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.179339 restraints weight = 19996.983| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.6732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21368 Z= 0.162 Angle : 0.640 14.838 28966 Z= 0.335 Chirality : 0.044 0.239 3246 Planarity : 0.004 0.042 3599 Dihedral : 10.439 172.349 2944 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.73 % Allowed : 18.50 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.17), residues: 2580 helix: 0.88 (0.15), residues: 1331 sheet: -1.75 (0.27), residues: 345 loop : -1.65 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 340 TYR 0.021 0.002 TYR B 165 PHE 0.018 0.002 PHE E 11 TRP 0.022 0.002 TRP E 20 HIS 0.005 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (21368) covalent geometry : angle 0.63956 / 0.34 (28966) hydrogen bonds : bond 0.03415 / 2.29 ( 1054) hydrogen bonds : angle 4.85906 / 3.43 ( 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 363 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 302 time to evaluate : 0.790 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: 0.5651 (m-40) cc_final: 0.5240 (m-40) REVERT: A 165 TYR cc_start: 0.7324 (m-10) cc_final: 0.6678 (m-10) REVERT: A 333 LYS cc_start: 0.6169 (OUTLIER) cc_final: 0.5379 (ttpt) REVERT: A 389 GLU cc_start: 0.5514 (OUTLIER) cc_final: 0.5306 (tt0) REVERT: B 103 MET cc_start: 0.6657 (mmm) cc_final: 0.6445 (mmm) REVERT: B 118 GLU cc_start: 0.7075 (tt0) cc_final: 0.6428 (mt-10) REVERT: B 138 MET cc_start: 0.7859 (mmm) cc_final: 0.7616 (mmm) REVERT: B 153 ASP cc_start: 0.7953 (t0) cc_final: 0.7651 (t70) REVERT: B 247 ASP cc_start: 0.6566 (m-30) cc_final: 0.6304 (m-30) REVERT: C 24 ASP cc_start: 0.7778 (m-30) cc_final: 0.7467 (m-30) REVERT: C 145 SER cc_start: 0.8740 (p) cc_final: 0.7981 (m) REVERT: D 264 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7151 (mt-10) REVERT: D 338 GLU cc_start: 0.8212 (tp30) cc_final: 0.7172 (mt-10) REVERT: D 419 MET cc_start: 0.7491 (mmt) cc_final: 0.7165 (mmt) REVERT: E 23 MET cc_start: 0.7534 (mmp) cc_final: 0.7115 (mmt) REVERT: E 138 MET cc_start: 0.8536 (tpt) cc_final: 0.8193 (tpt) REVERT: E 371 ILE cc_start: 0.7846 (OUTLIER) cc_final: 0.7340 (tp) REVERT: F 90 LEU cc_start: 0.6043 (OUTLIER) cc_final: 0.5582 (mm) REVERT: F 158 TYR cc_start: 0.5240 (p90) cc_final: 0.4937 (p90) REVERT: F 307 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8336 (mp) outliers start: 61 outliers final: 34 residues processed: 345 average time/residue: 0.1413 time to fit residues: 78.7638 Evaluate side-chains 318 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 279 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 265 LYS 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 377 LEU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 60 LEU 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 344 VAL 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 128 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 254 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 299 LEU 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 50 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 404 ILE 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: 5.9990 chunk 238 optimal weight: 0.9980 chunk 253 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 255 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 191 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 HIS ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.197525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.179027 restraints weight = 21209.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.178154 restraints weight = 32122.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.179705 restraints weight = 27025.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.179669 restraints weight = 17294.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.180231 restraints weight = 16839.570| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.6950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21368 Z= 0.149 Angle : 0.639 14.701 28966 Z= 0.332 Chirality : 0.043 0.237 3246 Planarity : 0.004 0.045 3599 Dihedral : 10.413 169.717 2944 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.28 % Allowed : 19.93 % Favored : 77.79 % 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: -0.46 (0.17), residues: 2580 helix: 1.03 (0.15), residues: 1329 sheet: -1.78 (0.27), residues: 346 loop : -1.67 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 177 TYR 0.023 0.002 TYR B 312 PHE 0.025 0.002 PHE C 16 TRP 0.042 0.002 TRP D 154 HIS 0.004 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (21368) covalent geometry : angle 0.63868 / 0.33 (28966) hydrogen bonds : bond 0.03286 / 2.21 ( 1054) hydrogen bonds : angle 4.81746 / 3.40 ( 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 336 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 285 time to evaluate : 0.747 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: 0.5620 (m-40) cc_final: 0.5141 (m-40) REVERT: A 165 TYR cc_start: 0.7336 (m-10) cc_final: 0.6703 (m-10) REVERT: A 333 LYS cc_start: 0.6063 (OUTLIER) cc_final: 0.5408 (ttpt) REVERT: A 389 GLU cc_start: 0.5599 (OUTLIER) cc_final: 0.5357 (tt0) REVERT: B 60 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7188 (mt) REVERT: B 95 GLU cc_start: 0.7533 (tp30) cc_final: 0.7075 (tt0) REVERT: B 118 GLU cc_start: 0.7135 (tt0) cc_final: 0.6463 (mt-10) REVERT: B 138 MET cc_start: 0.7855 (mmm) cc_final: 0.7263 (mmt) REVERT: C 92 LYS cc_start: 0.7593 (mmmm) cc_final: 0.7189 (tptt) REVERT: C 138 MET cc_start: 0.7506 (tpt) cc_final: 0.7081 (tpt) REVERT: C 145 SER cc_start: 0.8631 (p) cc_final: 0.8007 (m) REVERT: D 264 GLU cc_start: 0.7334 (mm-30) cc_final: 0.7115 (mt-10) REVERT: D 338 GLU cc_start: 0.8136 (tp30) cc_final: 0.7230 (mt-10) REVERT: E 23 MET cc_start: 0.7487 (mmp) cc_final: 0.7106 (mmt) REVERT: E 138 MET cc_start: 0.8536 (tpt) cc_final: 0.8149 (tpt) REVERT: E 371 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7307 (tp) REVERT: F 112 GLU cc_start: 0.6458 (mp0) cc_final: 0.6235 (mp0) REVERT: F 158 TYR cc_start: 0.5318 (p90) cc_final: 0.4951 (p90) outliers start: 51 outliers final: 34 residues processed: 320 average time/residue: 0.1370 time to fit residues: 70.8780 Evaluate side-chains 309 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 271 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 255 SER Chi-restraints excluded: chain A residue 265 LYS 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 B residue 60 LEU 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 C residue 19 VAL Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 356 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 254 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 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 50 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 404 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 0.9990 chunk 194 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 217 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN E 253 HIS ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.198061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.183110 restraints weight = 21181.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.176526 restraints weight = 32997.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.173763 restraints weight = 21122.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.174586 restraints weight = 19237.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.175100 restraints weight = 16351.728| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.7085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21368 Z= 0.144 Angle : 0.628 15.342 28966 Z= 0.326 Chirality : 0.043 0.252 3246 Planarity : 0.004 0.048 3599 Dihedral : 10.378 168.507 2944 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.28 % Allowed : 19.97 % Favored : 77.75 % 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: -0.38 (0.17), residues: 2580 helix: 1.12 (0.15), residues: 1332 sheet: -1.70 (0.28), residues: 333 loop : -1.71 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 340 TYR 0.017 0.001 TYR E 329 PHE 0.020 0.002 PHE C 16 TRP 0.051 0.002 TRP D 154 HIS 0.015 0.001 HIS E 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (21368) covalent geometry : angle 0.62841 / 0.33 (28966) hydrogen bonds : bond 0.03180 / 2.14 ( 1054) hydrogen bonds : angle 4.75157 / 3.35 ( 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 330 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 279 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.6460 (m-40) cc_final: 0.5850 (m-40) REVERT: A 165 TYR cc_start: 0.7413 (m-10) cc_final: 0.6707 (m-10) REVERT: A 333 LYS cc_start: 0.6066 (OUTLIER) cc_final: 0.5262 (ttpt) REVERT: A 389 GLU cc_start: 0.5849 (OUTLIER) cc_final: 0.5470 (tt0) REVERT: B 60 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7271 (mt) REVERT: B 95 GLU cc_start: 0.7591 (tp30) cc_final: 0.7141 (tt0) REVERT: B 118 GLU cc_start: 0.7209 (tt0) cc_final: 0.6367 (mt-10) REVERT: C 92 LYS cc_start: 0.7544 (mmmm) cc_final: 0.7137 (tptt) REVERT: C 138 MET cc_start: 0.7499 (tpt) cc_final: 0.7070 (tpt) REVERT: C 145 SER cc_start: 0.8699 (p) cc_final: 0.8074 (m) REVERT: D 1 MET cc_start: 0.7550 (ppp) cc_final: 0.7161 (ppp) REVERT: D 264 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7129 (mt-10) REVERT: D 338 GLU cc_start: 0.8031 (tp30) cc_final: 0.7176 (mt-10) REVERT: E 23 MET cc_start: 0.7527 (mmp) cc_final: 0.7168 (mmt) REVERT: E 138 MET cc_start: 0.8580 (tpt) cc_final: 0.8134 (tpt) REVERT: E 361 TRP cc_start: 0.7562 (OUTLIER) cc_final: 0.7197 (m-10) REVERT: E 371 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7285 (tp) REVERT: F 112 GLU cc_start: 0.6553 (mp0) cc_final: 0.6280 (mp0) REVERT: F 158 TYR cc_start: 0.5248 (p90) cc_final: 0.4827 (p90) REVERT: F 263 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.6366 (mmt) outliers start: 51 outliers final: 34 residues processed: 315 average time/residue: 0.1285 time to fit residues: 65.7959 Evaluate side-chains 308 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 268 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 265 LYS 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 19 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 128 MET 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 90 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 244 VAL 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 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 63 SER Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 404 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 35 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 0.3980 chunk 69 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN D 355 GLN E 253 HIS ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.194711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.176207 restraints weight = 21529.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.175596 restraints weight = 32906.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.176644 restraints weight = 28903.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.176355 restraints weight = 20441.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.177408 restraints weight = 18309.902| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.7349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21368 Z= 0.179 Angle : 0.664 15.060 28966 Z= 0.345 Chirality : 0.044 0.245 3246 Planarity : 0.004 0.047 3599 Dihedral : 10.499 169.248 2944 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.14 % Allowed : 20.24 % Favored : 77.61 % 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: -0.48 (0.17), residues: 2580 helix: 1.02 (0.15), residues: 1333 sheet: -1.72 (0.28), residues: 331 loop : -1.75 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 340 TYR 0.023 0.002 TYR B 312 PHE 0.025 0.002 PHE C 28 TRP 0.058 0.002 TRP D 154 HIS 0.022 0.001 HIS E 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (21368) covalent geometry : angle 0.66449 / 0.35 (28966) hydrogen bonds : bond 0.03310 / 2.23 ( 1054) hydrogen bonds : angle 4.84023 / 3.42 ( 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 325 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 277 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.5987 (m-40) cc_final: 0.5576 (m-40) REVERT: A 165 TYR cc_start: 0.7407 (m-10) cc_final: 0.6723 (m-10) REVERT: A 333 LYS cc_start: 0.6038 (OUTLIER) cc_final: 0.5246 (ttpt) REVERT: B 60 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7257 (mt) REVERT: B 95 GLU cc_start: 0.7611 (tp30) cc_final: 0.7184 (tt0) REVERT: B 118 GLU cc_start: 0.7323 (tt0) cc_final: 0.6462 (mt-10) REVERT: B 138 MET cc_start: 0.7901 (mmm) cc_final: 0.7664 (mmm) REVERT: C 92 LYS cc_start: 0.7658 (mmmm) cc_final: 0.7162 (tptt) REVERT: C 138 MET cc_start: 0.7692 (tpt) cc_final: 0.7315 (tpt) REVERT: C 145 SER cc_start: 0.8663 (p) cc_final: 0.8023 (m) REVERT: D 1 MET cc_start: 0.7504 (ppp) cc_final: 0.7219 (ppp) REVERT: D 264 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7114 (mt-10) REVERT: D 338 GLU cc_start: 0.8098 (tp30) cc_final: 0.7074 (mt-10) REVERT: E 23 MET cc_start: 0.7700 (mmp) cc_final: 0.7391 (mmt) REVERT: E 138 MET cc_start: 0.8590 (tpt) cc_final: 0.8255 (tpt) REVERT: E 361 TRP cc_start: 0.7560 (OUTLIER) cc_final: 0.7173 (m-10) REVERT: E 371 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7282 (tp) REVERT: F 112 GLU cc_start: 0.6474 (mp0) cc_final: 0.6198 (mp0) REVERT: F 158 TYR cc_start: 0.5485 (p90) cc_final: 0.5158 (p90) REVERT: F 263 MET cc_start: 0.7053 (OUTLIER) cc_final: 0.6479 (mmt) outliers start: 48 outliers final: 36 residues processed: 309 average time/residue: 0.1345 time to fit residues: 67.4372 Evaluate side-chains 312 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 271 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 255 SER Chi-restraints excluded: chain A residue 265 LYS 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 60 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 244 VAL 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 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 63 SER Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 404 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 29 optimal weight: 4.9990 chunk 214 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 184 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 chunk 238 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 216 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** 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 = 0.4209 r_free = 0.4209 target = 0.197104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.179239 restraints weight = 21199.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.179258 restraints weight = 29176.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.179178 restraints weight = 27429.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.178508 restraints weight = 20978.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.179206 restraints weight = 19710.373| |-----------------------------------------------------------------------------| r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.7453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21368 Z= 0.138 Angle : 0.632 15.613 28966 Z= 0.327 Chirality : 0.043 0.238 3246 Planarity : 0.004 0.047 3599 Dihedral : 10.419 167.662 2944 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.88 % Allowed : 20.96 % Favored : 77.17 % 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: -0.35 (0.17), residues: 2580 helix: 1.15 (0.15), residues: 1332 sheet: -1.68 (0.29), residues: 332 loop : -1.72 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 340 TYR 0.017 0.001 TYR A 47 PHE 0.021 0.002 PHE C 28 TRP 0.061 0.002 TRP D 154 HIS 0.005 0.001 HIS E 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (21368) covalent geometry : angle 0.63167 / 0.33 (28966) hydrogen bonds : bond 0.03136 / 2.11 ( 1054) hydrogen bonds : angle 4.71798 / 3.33 ( 3030) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3230.00 seconds wall clock time: 57 minutes 12.53 seconds (3432.53 seconds total)