Starting phenix.real_space_refine on Sun Aug 24 14:45:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g0z_29658/08_2025/8g0z_29658.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g0z_29658/08_2025/8g0z_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_2025/8g0z_29658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g0z_29658/08_2025/8g0z_29658.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g0z_29658/08_2025/8g0z_29658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g0z_29658/08_2025/8g0z_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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20944 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "B" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "C" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "D" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "E" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "F" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "M" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.61, per 1000 atoms: 0.27 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: 1.83 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 Processing helix chain 'A' and resid 13 through 20 Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 24 through 28 Processing helix chain 'A' and resid 31 through 47 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 66 through 79 Processing helix chain 'A' and resid 86 through 118 Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 176 through 183 Processing helix chain 'A' and resid 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: 3.97 Time building geometry restraints manager: 2.50 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=" N VAL E 19 " pdb=" CA VAL E 19 " ideal model delta sigma weight residual 1.452 1.492 -0.040 1.18e-02 7.18e+03 1.14e+01 bond pdb=" N SER F 225 " pdb=" CA SER F 225 " ideal model delta sigma weight residual 1.455 1.495 -0.041 1.25e-02 6.40e+03 1.07e+01 ... (remaining 21363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 28444 2.53 - 5.06: 490 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=" PB AGS E 501 " pdb=" O3B AGS E 501 " pdb=" PG AGS E 501 " ideal model delta sigma weight residual 120.12 131.99 -11.87 3.00e+00 1.11e-01 1.57e+01 angle pdb=" CA PHE D 383 " pdb=" CB PHE D 383 " pdb=" CG PHE D 383 " ideal model delta sigma weight residual 113.80 117.75 -3.95 1.00e+00 1.00e+00 1.56e+01 ... (remaining 28961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 12745 34.84 - 69.67: 174 69.67 - 104.51: 8 104.51 - 139.35: 1 139.35 - 174.18: 3 Dihedral angle restraints: 12931 sinusoidal: 5317 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 12928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2317 0.044 - 0.088: 570 0.088 - 0.132: 270 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.000 Find NCS groups from input model: 0.480 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 23.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5721 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= 0.361 Angle : 0.743 12.657 28966 Z= 0.503 Chirality : 0.051 0.220 3246 Planarity : 0.004 0.075 3599 Dihedral : 12.134 174.183 8011 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 aren 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 covalent geometry : bond 0.00507 (21368) covalent geometry : angle 0.74281 (28966) hydrogen bonds : bond 0.16624 ( 1054) hydrogen bonds : angle 6.57383 ( 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 : 0.518 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: 0.4830 (OUTLIER) cc_final: 0.4479 (tmmt) REVERT: B 43 HIS cc_start: 0.6384 (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: 0.7521 (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: 0.6929 (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: 0.1484 time to fit residues: 107.0069 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 : 0.593 ------------------------------------------------------------------------------- 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: 8.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4504 r_free = 0.4504 target = 0.233651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.220367 restraints weight = 21078.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.209540 restraints weight = 23767.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.209082 restraints weight = 23499.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.209450 restraints weight = 20522.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.209702 restraints weight = 17720.258| |-----------------------------------------------------------------------------| r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 21368 Z= 0.221 Angle : 0.703 8.124 28966 Z= 0.373 Chirality : 0.047 0.250 3246 Planarity : 0.004 0.040 3599 Dihedral : 10.879 174.522 3011 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.04 % Allowed : 11.39 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.17), residues: 2580 helix: 0.88 (0.14), residues: 1341 sheet: -0.80 (0.29), residues: 345 loop : -1.41 (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 0.026 0.003 PHE E 28 TRP 0.031 0.002 TRP E 266 HIS 0.007 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00505 (21368) covalent geometry : angle 0.70283 (28966) hydrogen bonds : bond 0.04105 ( 1054) hydrogen bonds : angle 5.14134 ( 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 385 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 317 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.6766 (tpp) cc_final: 0.6476 (tpp) REVERT: A 263 MET cc_start: 0.6426 (mmm) cc_final: 0.6204 (mmt) REVERT: A 333 LYS cc_start: 0.5909 (OUTLIER) cc_final: 0.5178 (ttpt) REVERT: B 8 HIS cc_start: 0.7119 (m90) cc_final: 0.6899 (m-70) REVERT: C 168 LYS cc_start: 0.6719 (mptt) cc_final: 0.6448 (mmmt) REVERT: C 204 SER cc_start: 0.8076 (OUTLIER) cc_final: 0.7682 (m) REVERT: D 23 MET cc_start: 0.8097 (mmm) cc_final: 0.7855 (mmt) REVERT: D 43 HIS cc_start: 0.7220 (t-90) cc_final: 0.6792 (t-90) REVERT: E 80 LEU cc_start: 0.5269 (OUTLIER) cc_final: 0.5039 (mt) REVERT: E 158 TYR cc_start: 0.5365 (p90) cc_final: 0.4875 (p90) REVERT: F 3 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6671 (mm-30) REVERT: F 112 GLU cc_start: 0.6082 (OUTLIER) cc_final: 0.5767 (mp0) REVERT: F 155 MET cc_start: 0.5944 (ptt) cc_final: 0.5413 (ptt) REVERT: F 165 TYR cc_start: 0.6953 (m-10) cc_final: 0.6220 (m-10) REVERT: F 418 LEU cc_start: 0.6391 (OUTLIER) cc_final: 0.6082 (mp) outliers start: 68 outliers final: 32 residues processed: 369 average time/residue: 0.1417 time to fit residues: 83.2663 Evaluate side-chains 294 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 257 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 B residue 19 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 145 SER 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: 0.8980 chunk 134 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 252 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 176 optimal weight: 8.9990 chunk 258 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN D 200 ASN F 288 ASN F 398 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.214612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.196999 restraints weight = 21070.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.196657 restraints weight = 29363.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.197183 restraints weight = 25491.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.197060 restraints weight = 18346.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.197883 restraints weight = 17680.251| |-----------------------------------------------------------------------------| r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 21368 Z= 0.195 Angle : 0.642 8.433 28966 Z= 0.339 Chirality : 0.045 0.203 3246 Planarity : 0.004 0.046 3599 Dihedral : 10.696 170.711 3005 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.26 % Allowed : 13.49 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.17), residues: 2580 helix: 0.82 (0.14), residues: 1339 sheet: -1.06 (0.28), residues: 340 loop : -1.50 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 236 TYR 0.022 0.002 TYR C 223 PHE 0.021 0.002 PHE F 383 TRP 0.030 0.002 TRP F 428 HIS 0.011 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00452 (21368) covalent geometry : angle 0.64218 (28966) hydrogen bonds : bond 0.04086 ( 1054) hydrogen bonds : angle 4.98144 ( 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 389 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 316 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ASN cc_start: 0.7473 (t0) cc_final: 0.7232 (t0) REVERT: A 333 LYS cc_start: 0.5975 (OUTLIER) cc_final: 0.5441 (ttpt) REVERT: B 46 GLU cc_start: 0.6623 (tt0) cc_final: 0.6350 (mt-10) REVERT: B 181 LYS cc_start: 0.7400 (pttt) cc_final: 0.7170 (pptt) REVERT: B 225 SER cc_start: 0.6965 (t) cc_final: 0.6714 (p) REVERT: C 24 ASP cc_start: 0.7834 (m-30) cc_final: 0.7368 (m-30) REVERT: C 147 ASP cc_start: 0.7120 (p0) cc_final: 0.6833 (p0) REVERT: C 168 LYS cc_start: 0.6865 (mptt) cc_final: 0.6544 (mmmt) REVERT: C 181 LYS cc_start: 0.7959 (ttpp) cc_final: 0.7462 (mtpt) REVERT: C 204 SER cc_start: 0.8107 (OUTLIER) cc_final: 0.7667 (m) REVERT: D 264 GLU cc_start: 0.7360 (mm-30) cc_final: 0.7072 (mt-10) REVERT: D 298 LYS cc_start: 0.6743 (mmtt) cc_final: 0.6501 (mtmt) REVERT: D 406 SER cc_start: 0.7486 (t) cc_final: 0.7025 (p) REVERT: E 137 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8283 (tt) REVERT: E 155 MET cc_start: 0.4255 (tpp) cc_final: 0.3954 (tpt) REVERT: E 158 TYR cc_start: 0.5464 (p90) cc_final: 0.4984 (p90) REVERT: E 371 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7130 (tp) REVERT: F 3 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6698 (tm-30) REVERT: F 47 TYR cc_start: 0.7755 (m-80) cc_final: 0.7539 (m-80) REVERT: F 90 LEU cc_start: 0.5403 (OUTLIER) cc_final: 0.5052 (mm) REVERT: F 155 MET cc_start: 0.5725 (OUTLIER) cc_final: 0.5520 (ptt) REVERT: F 165 TYR cc_start: 0.7106 (m-10) cc_final: 0.6105 (m-10) REVERT: F 241 MET cc_start: 0.7525 (mtm) cc_final: 0.7211 (mtm) REVERT: F 326 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7533 (mp0) outliers start: 73 outliers final: 29 residues processed: 373 average time/residue: 0.1348 time to fit residues: 79.7243 Evaluate side-chains 304 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 269 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 A residue 352 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain 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 155 MET Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 423 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 145 optimal weight: 0.0870 chunk 67 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 237 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 201 optimal weight: 4.9990 chunk 219 optimal weight: 6.9990 chunk 250 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 overall best weight: 2.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN C 295 ASN D 8 HIS D 200 ASN E 422 GLN E 426 GLN F 398 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.206833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.187963 restraints weight = 21261.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.187426 restraints weight = 31436.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.188130 restraints weight = 27910.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.188049 restraints weight = 18709.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.188286 restraints weight = 17660.351| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21368 Z= 0.187 Angle : 0.636 12.932 28966 Z= 0.333 Chirality : 0.044 0.258 3246 Planarity : 0.004 0.043 3599 Dihedral : 10.578 166.775 3001 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.99 % Allowed : 15.19 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.17), residues: 2580 helix: 0.84 (0.14), residues: 1336 sheet: -1.43 (0.28), residues: 347 loop : -1.52 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 340 TYR 0.027 0.002 TYR D 15 PHE 0.017 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 covalent geometry : bond 0.00435 (21368) covalent geometry : angle 0.63586 (28966) hydrogen bonds : bond 0.03563 ( 1054) hydrogen bonds : angle 4.91269 ( 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 383 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 316 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 LYS cc_start: 0.5880 (OUTLIER) cc_final: 0.5374 (ttpt) REVERT: A 389 GLU cc_start: 0.5558 (OUTLIER) cc_final: 0.5297 (tt0) REVERT: B 74 LYS cc_start: 0.7830 (tppt) cc_final: 0.7575 (tptp) REVERT: B 225 SER cc_start: 0.7109 (t) cc_final: 0.6726 (p) REVERT: C 24 ASP cc_start: 0.7896 (m-30) cc_final: 0.7414 (m-30) REVERT: C 142 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7584 (mp) REVERT: C 168 LYS cc_start: 0.6933 (mptt) cc_final: 0.6547 (mmmt) REVERT: C 181 LYS cc_start: 0.7998 (ttpp) cc_final: 0.7514 (mtpt) REVERT: C 226 MET cc_start: 0.8088 (mmp) cc_final: 0.7852 (mmp) REVERT: D 264 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7091 (mt-10) REVERT: D 406 SER cc_start: 0.7907 (t) cc_final: 0.7432 (p) REVERT: E 80 LEU cc_start: 0.5543 (OUTLIER) cc_final: 0.5339 (mt) REVERT: E 155 MET cc_start: 0.4399 (tpp) cc_final: 0.4069 (tpt) REVERT: E 158 TYR cc_start: 0.5563 (p90) cc_final: 0.5209 (p90) REVERT: E 371 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7182 (tp) REVERT: F 3 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6908 (mm-30) REVERT: F 53 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7870 (mm) REVERT: F 90 LEU cc_start: 0.5916 (OUTLIER) cc_final: 0.5558 (mm) REVERT: F 112 GLU cc_start: 0.6148 (mp0) cc_final: 0.5925 (mp0) REVERT: F 307 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8260 (mp) REVERT: F 326 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7623 (mp0) outliers start: 67 outliers final: 32 residues processed: 363 average time/residue: 0.1204 time to fit residues: 69.7072 Evaluate side-chains 320 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 280 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 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 352 THR Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 389 GLU 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 142 LEU Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 80 LEU 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 299 LEU 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 53 ILE 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 307 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 2 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 188 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 399 GLN F 398 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.205357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.186692 restraints weight = 20943.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.186098 restraints weight = 28873.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.187435 restraints weight = 25408.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.186200 restraints weight = 20812.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.186855 restraints weight = 17156.340| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.5674 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= 0.146 Angle : 0.602 12.879 28966 Z= 0.314 Chirality : 0.043 0.251 3246 Planarity : 0.004 0.036 3599 Dihedral : 10.439 164.112 3001 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.77 % Allowed : 16.89 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.17), residues: 2580 helix: 1.03 (0.15), residues: 1337 sheet: -1.48 (0.28), residues: 347 loop : -1.49 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 340 TYR 0.021 0.001 TYR D 15 PHE 0.019 0.002 PHE E 11 TRP 0.025 0.002 TRP E 20 HIS 0.004 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00334 (21368) covalent geometry : angle 0.60157 (28966) hydrogen bonds : bond 0.03308 ( 1054) hydrogen bonds : angle 4.76372 ( 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 370 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 308 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.7376 (tpt) cc_final: 0.7134 (mmm) REVERT: A 333 LYS cc_start: 0.6101 (OUTLIER) cc_final: 0.5451 (ttpt) REVERT: A 389 GLU cc_start: 0.5488 (OUTLIER) cc_final: 0.5281 (tt0) REVERT: B 95 GLU cc_start: 0.7450 (tp30) cc_final: 0.7246 (tp30) REVERT: C 24 ASP cc_start: 0.7865 (m-30) cc_final: 0.7430 (m-30) REVERT: C 181 LYS cc_start: 0.8039 (ttpp) cc_final: 0.7517 (mtpt) REVERT: D 1 MET cc_start: 0.7427 (ppp) cc_final: 0.7175 (ppp) REVERT: D 298 LYS cc_start: 0.6918 (mmtt) cc_final: 0.6519 (mtmt) REVERT: D 338 GLU cc_start: 0.8083 (tp30) cc_final: 0.7221 (mt-10) REVERT: D 419 MET cc_start: 0.7154 (mmt) cc_final: 0.6840 (mmt) REVERT: E 138 MET cc_start: 0.8303 (tpt) cc_final: 0.8086 (tpt) REVERT: E 158 TYR cc_start: 0.5572 (p90) cc_final: 0.5230 (p90) REVERT: E 371 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7251 (tp) REVERT: F 3 GLU cc_start: 0.7229 (mm-30) cc_final: 0.7017 (mm-30) REVERT: F 90 LEU cc_start: 0.5338 (OUTLIER) cc_final: 0.5072 (mm) REVERT: F 307 ILE cc_start: 0.8562 (mm) cc_final: 0.8276 (mp) outliers start: 62 outliers final: 37 residues processed: 353 average time/residue: 0.1278 time to fit residues: 71.2619 Evaluate side-chains 322 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 281 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 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 352 THR Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 196 MET 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 196 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 243 ASP Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain F residue 18 LYS 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 140 GLN Chi-restraints excluded: chain F residue 404 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 243 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 175 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 177 optimal weight: 8.9990 chunk 227 optimal weight: 4.9990 chunk 174 optimal weight: 0.4980 chunk 135 optimal weight: 6.9990 chunk 179 optimal weight: 10.0000 chunk 123 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 355 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN E 399 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.200678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.181809 restraints weight = 21366.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.181264 restraints weight = 32863.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.182356 restraints weight = 27161.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.181388 restraints weight = 21405.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.182855 restraints weight = 17725.727| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.6202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21368 Z= 0.171 Angle : 0.629 14.939 28966 Z= 0.326 Chirality : 0.043 0.224 3246 Planarity : 0.004 0.040 3599 Dihedral : 10.506 162.022 3001 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.90 % Allowed : 18.36 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.17), residues: 2580 helix: 0.99 (0.15), residues: 1332 sheet: -1.59 (0.28), residues: 345 loop : -1.55 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 340 TYR 0.029 0.002 TYR B 15 PHE 0.019 0.002 PHE E 11 TRP 0.023 0.002 TRP E 20 HIS 0.007 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00400 (21368) covalent geometry : angle 0.62861 (28966) hydrogen bonds : bond 0.03330 ( 1054) hydrogen bonds : angle 4.79913 ( 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 370 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 305 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 THR cc_start: 0.6776 (OUTLIER) cc_final: 0.6447 (m) REVERT: A 165 TYR cc_start: 0.7357 (m-10) cc_final: 0.6686 (m-10) REVERT: A 333 LYS cc_start: 0.5891 (OUTLIER) cc_final: 0.5140 (ttpt) REVERT: A 389 GLU cc_start: 0.5782 (OUTLIER) cc_final: 0.5420 (tt0) REVERT: C 24 ASP cc_start: 0.7984 (m-30) cc_final: 0.7590 (m-30) REVERT: C 142 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7530 (mp) REVERT: C 181 LYS cc_start: 0.8106 (ttpp) cc_final: 0.7579 (mtpt) REVERT: D 1 MET cc_start: 0.7351 (ppp) cc_final: 0.7134 (ppp) REVERT: D 154 TRP cc_start: 0.7510 (t60) cc_final: 0.7122 (t60) REVERT: D 155 MET cc_start: 0.8487 (mmm) cc_final: 0.8219 (tpp) REVERT: E 23 MET cc_start: 0.7259 (mmp) cc_final: 0.6917 (mmt) REVERT: E 148 SER cc_start: 0.6940 (p) cc_final: 0.6706 (p) REVERT: E 158 TYR cc_start: 0.5580 (p90) cc_final: 0.5353 (p90) REVERT: E 371 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7366 (tp) REVERT: F 3 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7091 (mm-30) REVERT: F 90 LEU cc_start: 0.5797 (OUTLIER) cc_final: 0.5439 (mm) REVERT: F 112 GLU cc_start: 0.6329 (mp0) cc_final: 0.6118 (mp0) REVERT: F 307 ILE cc_start: 0.8492 (mm) cc_final: 0.8208 (mp) REVERT: F 392 GLU cc_start: 0.6062 (OUTLIER) cc_final: 0.5704 (pt0) outliers start: 65 outliers final: 37 residues processed: 353 average time/residue: 0.1269 time to fit residues: 72.0769 Evaluate side-chains 324 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 280 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 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 352 THR Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 204 SER 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 199 VAL Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 265 LYS 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 18 LYS 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 392 GLU 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: 9.9990 chunk 99 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 6 optimal weight: 20.0000 chunk 133 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 227 optimal weight: 0.9980 chunk 243 optimal weight: 6.9990 chunk 253 optimal weight: 6.9990 chunk 223 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN E 399 GLN E 403 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.198083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.179695 restraints weight = 21323.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.178399 restraints weight = 30988.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.179615 restraints weight = 27585.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.179228 restraints weight = 20110.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.179343 restraints weight = 19876.259| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.6625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21368 Z= 0.164 Angle : 0.627 13.572 28966 Z= 0.327 Chirality : 0.043 0.235 3246 Planarity : 0.004 0.043 3599 Dihedral : 10.439 159.698 2999 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.99 % Allowed : 18.41 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.17), residues: 2580 helix: 1.04 (0.15), residues: 1331 sheet: -1.69 (0.27), residues: 353 loop : -1.57 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 340 TYR 0.022 0.002 TYR D 15 PHE 0.017 0.002 PHE A 11 TRP 0.020 0.002 TRP E 154 HIS 0.004 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00385 (21368) covalent geometry : angle 0.62731 (28966) hydrogen bonds : bond 0.03274 ( 1054) hydrogen bonds : angle 4.79218 ( 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 364 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 297 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 THR cc_start: 0.6936 (OUTLIER) cc_final: 0.6575 (m) REVERT: A 128 MET cc_start: 0.6693 (tpp) cc_final: 0.6425 (tpt) REVERT: A 165 TYR cc_start: 0.7396 (m-10) cc_final: 0.6726 (m-10) REVERT: A 333 LYS cc_start: 0.6066 (OUTLIER) cc_final: 0.5444 (ttpt) REVERT: A 389 GLU cc_start: 0.5555 (OUTLIER) cc_final: 0.5227 (tt0) REVERT: B 74 LYS cc_start: 0.7838 (tptp) cc_final: 0.7310 (tppt) REVERT: B 138 MET cc_start: 0.7911 (mmm) cc_final: 0.7586 (mmm) REVERT: B 155 MET cc_start: 0.7792 (tpp) cc_final: 0.7480 (tpp) REVERT: C 24 ASP cc_start: 0.7786 (m-30) cc_final: 0.7458 (m-30) REVERT: C 92 LYS cc_start: 0.7520 (mmmm) cc_final: 0.7183 (tptt) REVERT: C 142 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7519 (mp) REVERT: C 145 SER cc_start: 0.8687 (p) cc_final: 0.8175 (m) REVERT: C 181 LYS cc_start: 0.7938 (ttpp) cc_final: 0.7538 (mtpt) REVERT: C 226 MET cc_start: 0.7960 (mmp) cc_final: 0.7758 (mmp) REVERT: D 338 GLU cc_start: 0.8243 (tp30) cc_final: 0.7361 (mt-10) REVERT: D 419 MET cc_start: 0.7208 (mmt) cc_final: 0.6905 (mmt) REVERT: E 23 MET cc_start: 0.7308 (mmp) cc_final: 0.7008 (mmt) REVERT: E 80 LEU cc_start: 0.5279 (OUTLIER) cc_final: 0.4785 (mt) REVERT: E 371 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7325 (tp) REVERT: F 90 LEU cc_start: 0.5967 (OUTLIER) cc_final: 0.5596 (mm) REVERT: F 307 ILE cc_start: 0.8619 (mm) cc_final: 0.8365 (mp) outliers start: 67 outliers final: 41 residues processed: 344 average time/residue: 0.1146 time to fit residues: 63.4654 Evaluate side-chains 326 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 278 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 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 352 THR 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 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 387 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 301 LYS 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 E residue 429 VAL Chi-restraints excluded: chain F residue 18 LYS 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 263 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 142 optimal weight: 0.7980 chunk 209 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 253 optimal weight: 8.9990 chunk 166 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 255 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 191 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN E 253 HIS 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 = 0.197896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.182989 restraints weight = 21367.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.182557 restraints weight = 31157.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.182820 restraints weight = 30033.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.182889 restraints weight = 23599.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.182997 restraints weight = 20410.922| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.6931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21368 Z= 0.156 Angle : 0.629 14.488 28966 Z= 0.326 Chirality : 0.043 0.197 3246 Planarity : 0.004 0.046 3599 Dihedral : 10.419 157.278 2999 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.04 % Allowed : 18.95 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.17), residues: 2580 helix: 1.07 (0.15), residues: 1331 sheet: -1.71 (0.27), residues: 348 loop : -1.58 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 177 TYR 0.022 0.002 TYR D 15 PHE 0.022 0.002 PHE C 16 TRP 0.047 0.002 TRP D 154 HIS 0.004 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00361 (21368) covalent geometry : angle 0.62896 (28966) hydrogen bonds : bond 0.03204 ( 1054) hydrogen bonds : angle 4.76435 ( 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 358 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 290 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.6799 (tpp) cc_final: 0.6563 (tpt) REVERT: A 165 TYR cc_start: 0.7306 (m-10) cc_final: 0.6674 (m-10) REVERT: A 333 LYS cc_start: 0.6051 (OUTLIER) cc_final: 0.5437 (ttpt) REVERT: A 389 GLU cc_start: 0.5421 (OUTLIER) cc_final: 0.5173 (tt0) REVERT: A 398 GLN cc_start: 0.5893 (pm20) cc_final: 0.5629 (pm20) REVERT: B 3 GLU cc_start: 0.6511 (mt-10) cc_final: 0.6270 (mp0) REVERT: B 118 GLU cc_start: 0.7202 (tt0) cc_final: 0.6452 (mt-10) REVERT: B 138 MET cc_start: 0.7838 (mmm) cc_final: 0.7520 (mmm) REVERT: C 24 ASP cc_start: 0.7740 (m-30) cc_final: 0.7423 (m-30) REVERT: C 92 LYS cc_start: 0.7561 (mmmm) cc_final: 0.7190 (tptt) REVERT: C 142 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7590 (mp) REVERT: C 181 LYS cc_start: 0.7995 (ttpp) cc_final: 0.7630 (mtpt) REVERT: D 1 MET cc_start: 0.7544 (ppp) cc_final: 0.7134 (ppp) REVERT: D 338 GLU cc_start: 0.8276 (tp30) cc_final: 0.7408 (mt-10) REVERT: D 419 MET cc_start: 0.7258 (mmt) cc_final: 0.6946 (mmt) REVERT: E 138 MET cc_start: 0.8672 (tpt) cc_final: 0.8338 (tpt) REVERT: E 361 TRP cc_start: 0.7569 (OUTLIER) cc_final: 0.7184 (m-10) REVERT: E 371 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7329 (tp) REVERT: F 90 LEU cc_start: 0.6103 (OUTLIER) cc_final: 0.5698 (mm) outliers start: 68 outliers final: 42 residues processed: 337 average time/residue: 0.1241 time to fit residues: 68.0953 Evaluate side-chains 324 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 276 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 389 GLU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 201 VAL 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 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 18 LYS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain F residue 263 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 0.8980 chunk 194 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.196801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.179042 restraints weight = 21354.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.178031 restraints weight = 28859.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.178731 restraints weight = 26967.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.178077 restraints weight = 23515.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.178681 restraints weight = 19708.753| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.7112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21368 Z= 0.157 Angle : 0.641 14.737 28966 Z= 0.332 Chirality : 0.043 0.241 3246 Planarity : 0.004 0.045 3599 Dihedral : 10.417 156.135 2999 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.73 % Allowed : 19.08 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.17), residues: 2580 helix: 1.09 (0.15), residues: 1333 sheet: -1.71 (0.28), residues: 351 loop : -1.60 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 340 TYR 0.021 0.002 TYR F 15 PHE 0.019 0.002 PHE C 16 TRP 0.059 0.002 TRP D 154 HIS 0.020 0.001 HIS E 253 Details of bonding type rmsd covalent geometry : bond 0.00368 (21368) covalent geometry : angle 0.64101 (28966) hydrogen bonds : bond 0.03205 ( 1054) hydrogen bonds : angle 4.76482 ( 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 342 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 281 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.5594 (m-40) cc_final: 0.5284 (m-40) REVERT: A 139 ARG cc_start: 0.6271 (OUTLIER) cc_final: 0.5988 (tpt170) REVERT: A 165 TYR cc_start: 0.7425 (m-10) cc_final: 0.6776 (m-10) REVERT: A 333 LYS cc_start: 0.6048 (OUTLIER) cc_final: 0.5433 (ttpt) REVERT: A 398 GLN cc_start: 0.6004 (pm20) cc_final: 0.5743 (pm20) REVERT: B 3 GLU cc_start: 0.6497 (mt-10) cc_final: 0.6263 (mp0) REVERT: B 74 LYS cc_start: 0.7986 (tptp) cc_final: 0.7583 (tppt) REVERT: B 118 GLU cc_start: 0.7257 (tt0) cc_final: 0.6474 (mt-10) REVERT: B 138 MET cc_start: 0.7900 (mmm) cc_final: 0.7540 (mmm) REVERT: B 155 MET cc_start: 0.7914 (tpp) cc_final: 0.7625 (tpp) REVERT: C 92 LYS cc_start: 0.7586 (mmmm) cc_final: 0.7181 (tptt) REVERT: C 138 MET cc_start: 0.7572 (tpt) cc_final: 0.7266 (tpt) REVERT: C 142 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7542 (mp) REVERT: C 145 SER cc_start: 0.8708 (p) cc_final: 0.8208 (m) REVERT: D 1 MET cc_start: 0.7505 (ppp) cc_final: 0.7152 (ppp) REVERT: D 338 GLU cc_start: 0.8161 (tp30) cc_final: 0.7319 (mt-10) REVERT: D 419 MET cc_start: 0.7310 (mmt) cc_final: 0.6939 (mmt) REVERT: E 80 LEU cc_start: 0.5260 (OUTLIER) cc_final: 0.4911 (mt) REVERT: E 138 MET cc_start: 0.8655 (tpt) cc_final: 0.8336 (tpt) REVERT: E 301 LYS cc_start: 0.3975 (pttt) cc_final: 0.3724 (mmtt) REVERT: E 361 TRP cc_start: 0.7581 (OUTLIER) cc_final: 0.7184 (m-10) REVERT: E 371 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7308 (tp) REVERT: E 384 MET cc_start: 0.6744 (mmm) cc_final: 0.6497 (mmm) REVERT: F 90 LEU cc_start: 0.6092 (OUTLIER) cc_final: 0.5673 (mm) outliers start: 61 outliers final: 37 residues processed: 323 average time/residue: 0.1193 time to fit residues: 62.1597 Evaluate side-chains 312 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 268 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 139 ARG 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 421 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 142 LEU 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 199 VAL Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 265 LYS 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 58 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 90 LEU 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: 0.5980 chunk 68 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 26 optimal weight: 0.4980 chunk 180 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 chunk 139 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN D 355 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.198732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.180617 restraints weight = 21233.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.179838 restraints weight = 29636.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.181232 restraints weight = 26003.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.180017 restraints weight = 20273.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.180286 restraints weight = 20094.984| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.7220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21368 Z= 0.131 Angle : 0.632 14.812 28966 Z= 0.325 Chirality : 0.042 0.161 3246 Planarity : 0.003 0.046 3599 Dihedral : 10.268 153.515 2999 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.88 % Allowed : 19.71 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.17), residues: 2580 helix: 1.23 (0.15), residues: 1332 sheet: -1.57 (0.29), residues: 334 loop : -1.62 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 340 TYR 0.020 0.001 TYR D 15 PHE 0.019 0.002 PHE C 16 TRP 0.055 0.002 TRP D 154 HIS 0.005 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00299 (21368) covalent geometry : angle 0.63175 (28966) hydrogen bonds : bond 0.03084 ( 1054) hydrogen bonds : angle 4.68637 ( 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 319 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 277 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 TYR cc_start: 0.7379 (m-10) cc_final: 0.6747 (m-10) REVERT: A 333 LYS cc_start: 0.6001 (OUTLIER) cc_final: 0.5392 (ttpt) REVERT: B 3 GLU cc_start: 0.6502 (mt-10) cc_final: 0.6254 (mp0) REVERT: B 74 LYS cc_start: 0.7962 (tptp) cc_final: 0.7529 (tppt) REVERT: B 118 GLU cc_start: 0.7185 (tt0) cc_final: 0.6380 (mt-10) REVERT: C 138 MET cc_start: 0.7559 (tpt) cc_final: 0.7359 (tpt) REVERT: D 1 MET cc_start: 0.7452 (ppp) cc_final: 0.7232 (ppp) REVERT: D 338 GLU cc_start: 0.8070 (tp30) cc_final: 0.7280 (mt-10) REVERT: E 23 MET cc_start: 0.7758 (mmp) cc_final: 0.7379 (mmt) REVERT: E 80 LEU cc_start: 0.5230 (OUTLIER) cc_final: 0.4892 (mt) REVERT: E 138 MET cc_start: 0.8638 (tpt) cc_final: 0.8338 (tpt) REVERT: E 361 TRP cc_start: 0.7506 (OUTLIER) cc_final: 0.7086 (m-10) REVERT: E 371 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7376 (tp) REVERT: F 90 LEU cc_start: 0.5674 (OUTLIER) cc_final: 0.5326 (mm) REVERT: F 166 MET cc_start: 0.6024 (ptm) cc_final: 0.5817 (mtp) outliers start: 42 outliers final: 31 residues processed: 309 average time/residue: 0.1229 time to fit residues: 62.4753 Evaluate side-chains 299 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 263 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 163 LEU 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 421 VAL Chi-restraints excluded: chain B residue 19 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 75 THR Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 265 LYS 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 58 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 366 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 29 optimal weight: 0.9990 chunk 214 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 184 optimal weight: 0.0980 chunk 33 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 238 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 216 optimal weight: 0.7980 chunk 37 optimal weight: 10.0000 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.200259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.181257 restraints weight = 21022.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.179669 restraints weight = 30281.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.180429 restraints weight = 27713.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.177634 restraints weight = 22864.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.179174 restraints weight = 18985.295| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.7328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21368 Z= 0.124 Angle : 0.626 14.796 28966 Z= 0.321 Chirality : 0.042 0.191 3246 Planarity : 0.003 0.046 3599 Dihedral : 10.169 153.244 2999 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.65 % Allowed : 20.06 % Favored : 78.28 % 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 aren not related in a simple way. whole: -0.11 (0.17), residues: 2580 helix: 1.31 (0.15), residues: 1334 sheet: -1.47 (0.29), residues: 337 loop : -1.58 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 340 TYR 0.047 0.002 TYR F 165 PHE 0.018 0.001 PHE C 16 TRP 0.063 0.002 TRP D 154 HIS 0.005 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00280 (21368) covalent geometry : angle 0.62602 (28966) hydrogen bonds : bond 0.02994 ( 1054) hydrogen bonds : angle 4.65406 ( 3030) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2884.13 seconds wall clock time: 51 minutes 12.20 seconds (3072.20 seconds total)