Starting phenix.real_space_refine on Sat Jul 4 12:43:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dtp_27707/07_2026/8dtp_27707.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dtp_27707/07_2026/8dtp_27707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dtp_27707/07_2026/8dtp_27707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dtp_27707/07_2026/8dtp_27707.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dtp_27707/07_2026/8dtp_27707.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dtp_27707/07_2026/8dtp_27707.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dtp_27707/07_2026/8dtp_27707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dtp_27707/07_2026/8dtp_27707.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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 3469 2.21 5 O 4080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20944 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "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: 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: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.63, per 1000 atoms: 0.22 Number of scatterers: 20944 At special positions: 0 Unit cell: (112.608, 134.136, 141.588, 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 4080 8.00 N 3469 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: 1.80 Conformation dependent library (CDL) restraints added in 763.5 milliseconds 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4920 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 16 sheets defined 55.7% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 Processing helix chain 'A' and resid 13 through 20 Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 24 through 28 Processing helix chain 'A' and resid 31 through 47 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 66 through 79 Processing helix chain 'A' and resid 86 through 118 Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 176 through 183 Processing helix chain 'A' and resid 202 through 217 removed outlier: 4.527A pdb=" N GLY A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 243 Processing helix chain 'A' and resid 245 through 252 removed outlier: 3.520A pdb=" N ILE A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 269 removed outlier: 3.549A 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: 3.568A pdb=" N ASP B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 Processing helix chain 'B' and resid 255 through 269 removed outlier: 3.844A pdb=" N LYS B 269 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 301 Processing helix chain 'B' and resid 327 through 347 removed outlier: 3.589A pdb=" N THR B 331 " --> pdb=" O ASN B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'B' and resid 391 through 396 removed outlier: 3.628A pdb=" N ALA B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 13 through 20 Processing helix chain 'C' and resid 24 through 28 removed outlier: 3.769A pdb=" N PHE C 28 " --> pdb=" O SER C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 47 Processing helix chain 'C' and resid 52 through 63 Processing helix chain 'C' and resid 66 through 77 removed outlier: 4.001A pdb=" N GLY C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 119 Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 133 through 143 Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 229 through 242 Processing helix chain 'C' and resid 245 through 252 Processing helix chain 'C' and resid 255 through 268 Processing helix chain 'C' and resid 286 through 301 Processing helix chain 'C' and resid 312 through 316 removed outlier: 3.639A pdb=" N ILE C 315 " --> pdb=" O TYR C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 347 Processing helix chain 'C' and resid 357 through 361 removed outlier: 3.653A pdb=" N TRP C 361 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 375 through 381 removed outlier: 3.956A 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: 3.503A pdb=" N TYR D 27 " --> pdb=" O ASP D 24 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE D 28 " --> pdb=" O SER D 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 24 through 28' Processing helix chain 'D' and resid 31 through 48 Processing helix chain 'D' and resid 52 through 62 Processing helix chain 'D' and resid 66 through 80 Processing helix chain 'D' and resid 86 through 118 Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 133 through 143 removed outlier: 3.936A pdb=" N ILE D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 163 Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 204 through 217 Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'D' and resid 245 through 252 Processing helix chain 'D' and resid 255 through 268 Processing helix chain 'D' and resid 286 through 301 Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 327 through 347 Processing helix chain 'D' and resid 357 through 361 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'D' and resid 375 through 380 removed outlier: 4.004A pdb=" N ALA D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 396 Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 12 through 20 removed outlier: 3.593A 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: 3.534A pdb=" N ALA E 141 " --> pdb=" O ILE E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 166 Processing helix chain 'E' and resid 176 through 184 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 229 through 243 Processing helix chain 'E' and resid 246 through 251 removed outlier: 3.587A pdb=" N ASP E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 269 Processing helix chain 'E' and resid 286 through 301 Processing helix chain 'E' and resid 327 through 347 removed outlier: 3.843A pdb=" N LYS E 333 " --> pdb=" O TYR E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 361 Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 390 through 397 Processing helix chain 'F' and resid 2 through 12 Processing helix chain 'F' and resid 13 through 20 Processing helix chain 'F' and resid 21 through 23 No H-bonds generated for 'chain 'F' and resid 21 through 23' Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 31 through 48 removed outlier: 3.759A pdb=" N ASN F 35 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 62 Processing helix chain 'F' and resid 66 through 80 Processing helix chain 'F' and resid 88 through 118 removed outlier: 3.902A 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: 3.660A pdb=" N LEU F 142 " --> pdb=" O MET F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 167 Processing helix chain 'F' and resid 176 through 184 Processing helix chain 'F' and resid 202 through 216 Processing helix chain 'F' and resid 229 through 243 Processing helix chain 'F' and resid 245 through 252 Processing helix chain 'F' and resid 255 through 269 removed outlier: 3.706A pdb=" N LYS F 269 " --> pdb=" O LYS F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 302 Processing helix chain 'F' and resid 327 through 347 Processing helix chain 'F' and resid 376 through 381 Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 153 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: 6.224A 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: 3.626A pdb=" N PHE B 383 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS B 405 " --> pdb=" O MET B 384 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA3, first strand: chain 'A' and resid 427 through 429 removed outlier: 6.512A pdb=" N MET A 384 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU A 192 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N LEU A 385 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 194 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL A 387 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N MET A 196 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N THR A 191 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N THR A 352 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ASN A 193 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ALA A 354 " --> pdb=" O ASN A 193 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU A 195 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA A 353 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU A 222 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL A 221 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LYS A 278 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TYR A 223 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 152 through 153 removed outlier: 6.614A 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: 6.242A 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: 7.639A 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: 6.431A pdb=" N MET C 384 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 172 Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 422 Processing sheet with id=AA7, first strand: chain 'C' and resid 152 through 153 removed outlier: 6.511A pdb=" N VAL D 221 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 7.748A 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: 6.324A pdb=" N VAL E 194 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL E 387 " --> pdb=" O VAL E 194 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N MET E 196 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N MET E 384 " --> pdb=" O ILE E 404 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 171 through 172 Processing sheet with id=AB3, first strand: chain 'D' and resid 349 through 354 removed outlier: 6.038A pdb=" N THR D 191 " --> pdb=" O LEU D 350 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR D 352 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN D 193 " --> pdb=" O THR D 352 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ALA D 354 " --> pdb=" O ASN D 193 " (cutoff:3.500A) removed outlier: 5.929A 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: 6.439A pdb=" N VAL D 194 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL D 387 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N MET D 196 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 6.540A 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 349 through 352 removed outlier: 3.708A pdb=" N PHE F 383 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 275 through 279 removed outlier: 6.325A pdb=" N LEU F 222 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 419 through 422 1056 hydrogen bonds defined for protein. 3033 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: 3.91 Time building geometry restraints manager: 2.39 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: 5600 1.50 - 1.65: 8864 1.65 - 1.80: 98 1.80 - 1.95: 111 Bond restraints: 21368 Sorted by residual: bond pdb=" CE1 HIS C 253 " pdb=" NE2 HIS C 253 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.66e+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 1.52e+01 bond pdb=" CE1 HIS B 152 " pdb=" NE2 HIS B 152 " ideal model delta sigma weight residual 1.321 1.357 -0.036 1.00e-02 1.00e+04 1.27e+01 bond pdb=" N VAL E 19 " pdb=" CA VAL E 19 " ideal model delta sigma weight residual 1.452 1.492 -0.040 1.18e-02 7.18e+03 1.13e+01 bond pdb=" C3' DT M 16 " pdb=" C2' DT M 16 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 ... (remaining 21363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 27793 1.56 - 3.12: 1005 3.12 - 4.69: 142 4.69 - 6.25: 25 6.25 - 7.81: 1 Bond angle restraints: 28966 Sorted by residual: angle pdb=" N3 DT M 17 " pdb=" C4 DT M 17 " pdb=" O4 DT M 17 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT M 15 " pdb=" C4 DT M 15 " pdb=" O4 DT M 15 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT M 9 " pdb=" C4 DT M 9 " pdb=" O4 DT M 9 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT M 11 " pdb=" C4 DT M 11 " pdb=" O4 DT M 11 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT M 6 " pdb=" C4 DT M 6 " pdb=" O4 DT M 6 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 ... (remaining 28961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 12718 35.65 - 71.31: 149 71.31 - 106.96: 4 106.96 - 142.61: 1 142.61 - 178.27: 4 Dihedral angle restraints: 12876 sinusoidal: 5262 harmonic: 7614 Sorted by residual: dihedral pdb=" O1B AGS E 501 " pdb=" O3B AGS E 501 " pdb=" PB AGS E 501 " pdb=" PG AGS E 501 " ideal model delta sinusoidal sigma weight residual 68.91 -112.82 -178.27 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A AGS F 501 " pdb=" O3A AGS F 501 " pdb=" PA AGS F 501 " pdb=" PB AGS F 501 " ideal model delta sinusoidal sigma weight residual -67.73 106.47 -174.20 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 -88.57 157.48 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 12873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2392 0.044 - 0.088: 567 0.088 - 0.132: 243 0.132 - 0.175: 33 0.175 - 0.219: 11 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 1.20e+00 chirality pdb=" CA ARG A 124 " pdb=" N ARG A 124 " pdb=" C ARG A 124 " pdb=" CB ARG A 124 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ILE A 371 " pdb=" N ILE A 371 " pdb=" C ILE A 371 " pdb=" CB ILE A 371 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+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 3.34e-02 1.11e+01 pdb=" C GLU A 373 " 0.058 2.00e-02 2.50e+03 pdb=" O GLU A 373 " -0.021 2.00e-02 2.50e+03 pdb=" N SER A 374 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 145 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.14e+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 GLU A 122 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.36e+00 pdb=" C GLU A 122 " -0.036 2.00e-02 2.50e+03 pdb=" O GLU A 122 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS A 123 " 0.012 2.00e-02 2.50e+03 ... (remaining 3596 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 157 2.56 - 3.14: 16858 3.14 - 3.73: 33356 3.73 - 4.31: 46831 4.31 - 4.90: 78026 Nonbonded interactions: 175228 Sorted by model distance: nonbonded pdb=" O3B AGS B 501 " pdb="MG MG B 502 " model vdw 1.973 2.170 nonbonded pdb=" OE2 GLU B 227 " pdb="MG MG B 502 " model vdw 1.979 2.170 nonbonded pdb=" O2G AGS E 501 " pdb="MG MG E 502 " model vdw 1.984 2.170 nonbonded pdb=" O2B AGS F 501 " pdb="MG MG F 502 " model vdw 1.993 2.170 nonbonded pdb=" OE2 GLU C 227 " pdb="MG MG C 502 " model vdw 2.005 2.170 ... (remaining 175223 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 432) selection = (chain 'C' and resid 1 through 432) selection = (chain 'D' and resid 1 through 432) selection = (chain 'E' and resid 1 through 432) selection = (chain 'F' and resid 1 through 432) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.750 Find NCS groups from input model: 0.510 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:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21368 Z= 0.305 Angle : 0.640 7.809 28966 Z= 0.444 Chirality : 0.047 0.219 3246 Planarity : 0.004 0.075 3599 Dihedral : 11.930 178.266 7956 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.92 % Allowed : 6.26 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.17), residues: 2580 helix: 1.58 (0.15), residues: 1317 sheet: -0.15 (0.30), residues: 345 loop : -1.28 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 274 TYR 0.014 0.001 TYR E 329 PHE 0.023 0.002 PHE D 383 TRP 0.027 0.001 TRP F 351 HIS 0.008 0.001 HIS B 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.31 (21368) covalent geometry : angle 0.64049 / 0.44 (28966) hydrogen bonds : bond 0.15695 / 10.76 ( 1056) hydrogen bonds : angle 6.38349 / 4.56 ( 3033) *********************** 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 592 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 549 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8240 (tpt) cc_final: 0.7270 (tpt) REVERT: A 70 TYR cc_start: 0.6704 (t80) cc_final: 0.6445 (t80) REVERT: A 203 LYS cc_start: 0.7948 (mttm) cc_final: 0.7714 (mtmm) REVERT: A 312 TYR cc_start: 0.4815 (t80) cc_final: 0.4605 (t80) REVERT: A 337 GLU cc_start: 0.6337 (mt-10) cc_final: 0.6020 (mt-10) REVERT: B 13 GLN cc_start: 0.7676 (tp40) cc_final: 0.7475 (mp10) REVERT: B 53 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7568 (mm) REVERT: B 57 ASN cc_start: 0.7789 (p0) cc_final: 0.7453 (p0) REVERT: B 71 SER cc_start: 0.8308 (t) cc_final: 0.8103 (m) REVERT: B 92 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7959 (mmtp) REVERT: B 96 LYS cc_start: 0.8296 (mtpp) cc_final: 0.7948 (mttt) REVERT: B 109 LYS cc_start: 0.8213 (ttmm) cc_final: 0.7952 (tttt) REVERT: B 330 THR cc_start: 0.7601 (t) cc_final: 0.7358 (m) REVERT: C 92 LYS cc_start: 0.8106 (mmmm) cc_final: 0.7751 (mppt) REVERT: C 177 ARG cc_start: 0.7692 (mtm110) cc_final: 0.7478 (mtm110) REVERT: C 184 LYS cc_start: 0.7702 (mtpp) cc_final: 0.7455 (mtpt) REVERT: C 236 ARG cc_start: 0.8321 (mtt-85) cc_final: 0.7974 (mtp180) REVERT: C 279 GLN cc_start: 0.8193 (tt0) cc_final: 0.7880 (tt0) REVERT: C 313 LEU cc_start: 0.6143 (pp) cc_final: 0.5876 (tt) REVERT: C 317 LYS cc_start: 0.7867 (pttt) cc_final: 0.7623 (pttm) REVERT: D 86 ASP cc_start: 0.6867 (OUTLIER) cc_final: 0.5886 (t70) REVERT: D 153 ASP cc_start: 0.7384 (t0) cc_final: 0.7168 (t70) REVERT: D 177 ARG cc_start: 0.7803 (mtm110) cc_final: 0.7562 (mtm-85) REVERT: D 226 MET cc_start: 0.7580 (mmm) cc_final: 0.7264 (mmm) REVERT: D 227 GLU cc_start: 0.7202 (tt0) cc_final: 0.6785 (pm20) REVERT: D 238 ASP cc_start: 0.8633 (m-30) cc_final: 0.8401 (m-30) REVERT: D 279 GLN cc_start: 0.7722 (tt0) cc_final: 0.6829 (tm130) REVERT: D 331 THR cc_start: 0.7402 (p) cc_final: 0.6992 (m) REVERT: E 92 LYS cc_start: 0.8450 (tppp) cc_final: 0.8158 (ttmt) REVERT: E 109 LYS cc_start: 0.8056 (tptt) cc_final: 0.7715 (tttm) REVERT: E 170 ARG cc_start: 0.6466 (ptt-90) cc_final: 0.6036 (mtp85) REVERT: E 228 MET cc_start: 0.6478 (mmp) cc_final: 0.6160 (mmm) REVERT: E 265 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7756 (mppt) REVERT: E 274 ARG cc_start: 0.8026 (mtp180) cc_final: 0.7708 (mmm-85) REVERT: E 279 GLN cc_start: 0.7177 (pt0) cc_final: 0.6105 (tp40) REVERT: E 384 MET cc_start: 0.6712 (ttm) cc_final: 0.6491 (mtp) REVERT: E 392 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7136 (pm20) REVERT: E 413 LYS cc_start: 0.7861 (ttmt) cc_final: 0.7575 (mttt) REVERT: F 139 ARG cc_start: 0.7500 (ttm-80) cc_final: 0.6925 (ttp-110) REVERT: F 147 ASP cc_start: 0.7469 (m-30) cc_final: 0.7219 (p0) REVERT: F 247 ASP cc_start: 0.7450 (m-30) cc_final: 0.7111 (m-30) REVERT: F 302 ASN cc_start: 0.7693 (t0) cc_final: 0.7382 (t0) REVERT: F 327 ASN cc_start: 0.7051 (p0) cc_final: 0.6697 (p0) REVERT: F 333 LYS cc_start: 0.7406 (ttpp) cc_final: 0.6800 (ttmm) REVERT: F 347 GLU cc_start: 0.7100 (mp0) cc_final: 0.6882 (mm-30) REVERT: F 397 GLU cc_start: 0.6503 (tp30) cc_final: 0.6164 (tm-30) REVERT: F 398 GLN cc_start: 0.7540 (mt0) cc_final: 0.6940 (mp-120) REVERT: F 404 ILE cc_start: 0.8258 (mt) cc_final: 0.7976 (mm) REVERT: F 407 ARG cc_start: 0.6875 (ttp-170) cc_final: 0.6113 (ttm170) outliers start: 43 outliers final: 2 residues processed: 577 average time/residue: 0.6880 time to fit residues: 445.0158 Evaluate side-chains 328 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 323 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 380 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 258 optimal weight: 3.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN A 403 GLN C 116 ASN C 302 ASN D 116 ASN D 200 ASN ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN F 62 ASN F 140 GLN F 200 ASN F 295 ASN F 359 GLN F 399 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.174319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.144532 restraints weight = 23114.065| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.28 r_work: 0.3433 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2005 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= 0.190 Angle : 0.621 9.574 28966 Z= 0.330 Chirality : 0.044 0.226 3246 Planarity : 0.004 0.045 3599 Dihedral : 10.681 178.795 2950 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.29 % Allowed : 12.69 % Favored : 83.02 % 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 are not related in a simple way. whole: 0.42 (0.17), residues: 2580 helix: 1.39 (0.15), residues: 1348 sheet: -0.12 (0.29), residues: 353 loop : -1.27 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 322 TYR 0.018 0.002 TYR B 312 PHE 0.024 0.003 PHE D 65 TRP 0.014 0.001 TRP B 162 HIS 0.006 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (21368) covalent geometry : angle 0.62136 / 0.33 (28966) hydrogen bonds : bond 0.04393 / 2.94 ( 1056) hydrogen bonds : angle 5.01194 / 3.57 ( 3033) *********************** 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 441 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 345 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 ASP cc_start: 0.7289 (m-30) cc_final: 0.7073 (t0) REVERT: A 333 LYS cc_start: 0.7142 (mtpt) cc_final: 0.6768 (mmmt) REVERT: A 337 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6949 (mp0) REVERT: B 49 SER cc_start: 0.8773 (t) cc_final: 0.8502 (p) REVERT: B 92 LYS cc_start: 0.8436 (mmtt) cc_final: 0.8183 (mmtp) REVERT: B 96 LYS cc_start: 0.8438 (mtpp) cc_final: 0.8164 (mttt) REVERT: B 109 LYS cc_start: 0.8406 (ttmm) cc_final: 0.8162 (tttt) REVERT: C 92 LYS cc_start: 0.8174 (mmmm) cc_final: 0.7954 (mppt) REVERT: C 101 ARG cc_start: 0.8527 (mmm160) cc_final: 0.8324 (mmm160) REVERT: C 184 LYS cc_start: 0.8518 (mtpp) cc_final: 0.8293 (mtpt) REVERT: D 26 GLU cc_start: 0.7542 (mp0) cc_final: 0.7308 (mm-30) REVERT: D 136 ASP cc_start: 0.7191 (t70) cc_final: 0.6986 (t0) REVERT: D 139 ARG cc_start: 0.7631 (ttp80) cc_final: 0.6927 (ttp-110) REVERT: D 153 ASP cc_start: 0.7675 (t0) cc_final: 0.7292 (t70) REVERT: D 226 MET cc_start: 0.8082 (mmm) cc_final: 0.7777 (mmm) REVERT: D 331 THR cc_start: 0.7689 (p) cc_final: 0.7336 (m) REVERT: E 92 LYS cc_start: 0.8430 (tppp) cc_final: 0.8173 (ttmt) REVERT: E 109 LYS cc_start: 0.8155 (tptt) cc_final: 0.7778 (tttm) REVERT: E 170 ARG cc_start: 0.6730 (ptt-90) cc_final: 0.6064 (mtp85) REVERT: E 196 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7171 (ppp) REVERT: E 317 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.6677 (ptmt) REVERT: E 340 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7060 (ttp80) REVERT: E 392 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7481 (pp20) REVERT: E 413 LYS cc_start: 0.8034 (ttmt) cc_final: 0.7826 (mttt) REVERT: F 139 ARG cc_start: 0.7904 (ttm-80) cc_final: 0.7694 (ttp80) REVERT: F 147 ASP cc_start: 0.7576 (m-30) cc_final: 0.7275 (p0) REVERT: F 247 ASP cc_start: 0.7261 (m-30) cc_final: 0.7001 (m-30) REVERT: F 302 ASN cc_start: 0.7718 (t0) cc_final: 0.7374 (t0) REVERT: F 327 ASN cc_start: 0.6954 (p0) cc_final: 0.6571 (p0) REVERT: F 333 LYS cc_start: 0.7620 (ttpp) cc_final: 0.7194 (ttmt) REVERT: F 347 GLU cc_start: 0.7226 (mp0) cc_final: 0.6970 (mm-30) REVERT: F 368 MET cc_start: 0.5995 (mtp) cc_final: 0.5760 (mtt) REVERT: F 397 GLU cc_start: 0.6830 (tp30) cc_final: 0.6238 (tm-30) REVERT: F 398 GLN cc_start: 0.7463 (mt0) cc_final: 0.6933 (mp-120) REVERT: F 407 ARG cc_start: 0.7085 (ttp-170) cc_final: 0.6428 (ttm170) REVERT: F 431 ILE cc_start: 0.7155 (pp) cc_final: 0.6656 (pt) outliers start: 96 outliers final: 30 residues processed: 409 average time/residue: 0.6227 time to fit residues: 288.4595 Evaluate side-chains 316 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 283 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 317 LYS Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 321 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 147 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 17 optimal weight: 0.0980 chunk 252 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 258 optimal weight: 0.0970 chunk 62 optimal weight: 0.8980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 200 ASN C 288 ASN C 302 ASN D 13 GLN D 100 GLN D 200 ASN E 57 ASN E 167 ASN F 140 GLN F 200 ASN F 295 ASN F 359 GLN F 399 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.173982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.143123 restraints weight = 22367.666| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.18 r_work: 0.3433 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21368 Z= 0.144 Angle : 0.544 8.428 28966 Z= 0.294 Chirality : 0.042 0.225 3246 Planarity : 0.004 0.035 3599 Dihedral : 10.563 179.255 2942 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.07 % Allowed : 14.39 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.17), residues: 2580 helix: 1.54 (0.15), residues: 1353 sheet: 0.12 (0.30), residues: 334 loop : -1.32 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 177 TYR 0.014 0.001 TYR B 312 PHE 0.018 0.002 PHE D 65 TRP 0.013 0.001 TRP B 162 HIS 0.005 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (21368) covalent geometry : angle 0.54421 / 0.29 (28966) hydrogen bonds : bond 0.03834 / 2.57 ( 1056) hydrogen bonds : angle 4.78765 / 3.41 ( 3033) *********************** 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 399 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 308 time to evaluate : 0.923 Fit side-chains REVERT: A 136 ASP cc_start: 0.7401 (m-30) cc_final: 0.6967 (t0) REVERT: A 312 TYR cc_start: 0.5403 (t80) cc_final: 0.5173 (t80) REVERT: A 333 LYS cc_start: 0.7099 (ttpt) cc_final: 0.6772 (mmmt) REVERT: A 337 GLU cc_start: 0.7464 (mt-10) cc_final: 0.6998 (mp0) REVERT: A 427 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7745 (ttpp) REVERT: B 92 LYS cc_start: 0.8585 (mmtt) cc_final: 0.8264 (mmtp) REVERT: B 96 LYS cc_start: 0.8546 (mtpp) cc_final: 0.8198 (mttt) REVERT: B 109 LYS cc_start: 0.8558 (ttmm) cc_final: 0.8310 (tttt) REVERT: C 34 LYS cc_start: 0.7837 (tttt) cc_final: 0.7635 (tttp) REVERT: C 92 LYS cc_start: 0.8352 (mmmm) cc_final: 0.8034 (mppt) REVERT: C 128 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6510 (mtt) REVERT: D 1 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8193 (ptp) REVERT: D 3 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7546 (mp0) REVERT: D 26 GLU cc_start: 0.7703 (mp0) cc_final: 0.7432 (mp0) REVERT: D 86 ASP cc_start: 0.7078 (OUTLIER) cc_final: 0.6196 (t70) REVERT: D 136 ASP cc_start: 0.7344 (t70) cc_final: 0.7141 (t0) REVERT: D 153 ASP cc_start: 0.7822 (t0) cc_final: 0.7333 (t70) REVERT: D 226 MET cc_start: 0.8174 (mmm) cc_final: 0.7962 (mmm) REVERT: D 331 THR cc_start: 0.7670 (p) cc_final: 0.7330 (m) REVERT: E 92 LYS cc_start: 0.8495 (tppp) cc_final: 0.8169 (ttmt) REVERT: E 109 LYS cc_start: 0.8267 (tptt) cc_final: 0.7779 (tttp) REVERT: E 170 ARG cc_start: 0.6850 (ptt-90) cc_final: 0.6048 (mtp85) REVERT: E 340 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.6797 (ttp80) REVERT: E 371 ILE cc_start: 0.7721 (OUTLIER) cc_final: 0.7479 (pt) REVERT: E 392 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7442 (pp20) REVERT: E 413 LYS cc_start: 0.8134 (ttmt) cc_final: 0.7835 (mttt) REVERT: F 139 ARG cc_start: 0.8022 (ttm-80) cc_final: 0.7663 (ttp80) REVERT: F 147 ASP cc_start: 0.7722 (m-30) cc_final: 0.7291 (p0) REVERT: F 177 ARG cc_start: 0.6905 (mtm-85) cc_final: 0.6686 (mtm110) REVERT: F 302 ASN cc_start: 0.7716 (t0) cc_final: 0.7314 (t0) REVERT: F 327 ASN cc_start: 0.6729 (p0) cc_final: 0.6316 (p0) REVERT: F 333 LYS cc_start: 0.7569 (ttpp) cc_final: 0.7109 (ttmt) REVERT: F 347 GLU cc_start: 0.7323 (mp0) cc_final: 0.6932 (mm-30) REVERT: F 368 MET cc_start: 0.5716 (mtp) cc_final: 0.5408 (mtt) REVERT: F 370 ASP cc_start: 0.5857 (m-30) cc_final: 0.5593 (m-30) REVERT: F 397 GLU cc_start: 0.7007 (tp30) cc_final: 0.6206 (tm-30) REVERT: F 398 GLN cc_start: 0.7601 (mt0) cc_final: 0.6905 (mp-120) REVERT: F 407 ARG cc_start: 0.7148 (ttp-170) cc_final: 0.6446 (ttm170) REVERT: F 431 ILE cc_start: 0.7134 (pp) cc_final: 0.6680 (pt) outliers start: 91 outliers final: 36 residues processed: 372 average time/residue: 0.6355 time to fit residues: 268.6332 Evaluate side-chains 327 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 285 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 429 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 145 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 237 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 156 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 201 optimal weight: 9.9990 chunk 219 optimal weight: 0.4980 chunk 250 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 200 ASN B 288 ASN C 302 ASN D 100 GLN D 200 ASN E 167 ASN F 140 GLN F 200 ASN F 288 ASN F 295 ASN F 359 GLN F 399 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.175369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.144270 restraints weight = 22490.442| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.11 r_work: 0.3457 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21368 Z= 0.116 Angle : 0.514 7.548 28966 Z= 0.277 Chirality : 0.041 0.203 3246 Planarity : 0.003 0.041 3599 Dihedral : 10.520 179.023 2942 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.66 % Allowed : 15.46 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.17), residues: 2580 helix: 1.70 (0.15), residues: 1355 sheet: 0.11 (0.30), residues: 338 loop : -1.35 (0.19), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 139 TYR 0.017 0.001 TYR D 312 PHE 0.015 0.001 PHE D 65 TRP 0.012 0.001 TRP B 162 HIS 0.005 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (21368) covalent geometry : angle 0.51423 / 0.28 (28966) hydrogen bonds : bond 0.03406 / 2.29 ( 1056) hydrogen bonds : angle 4.61343 / 3.28 ( 3033) *********************** 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: 82 poor density : 301 time to evaluate : 0.866 Fit side-chains REVERT: A 79 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7969 (mtpm) REVERT: A 140 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7604 (mt0) REVERT: A 333 LYS cc_start: 0.7075 (ttpt) cc_final: 0.6842 (mmmt) REVERT: A 337 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7046 (mp0) REVERT: B 92 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8292 (mmtp) REVERT: B 96 LYS cc_start: 0.8521 (mtpp) cc_final: 0.8205 (mttt) REVERT: B 109 LYS cc_start: 0.8542 (ttmm) cc_final: 0.8301 (tttt) REVERT: B 274 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7255 (mtm-85) REVERT: C 92 LYS cc_start: 0.8345 (mmmm) cc_final: 0.8034 (mppt) REVERT: C 128 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.6512 (mtt) REVERT: D 1 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8148 (ptm) REVERT: D 3 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7592 (mp0) REVERT: D 153 ASP cc_start: 0.7755 (t0) cc_final: 0.7193 (t70) REVERT: D 226 MET cc_start: 0.8176 (mmm) cc_final: 0.7943 (mmm) REVERT: D 331 THR cc_start: 0.7641 (p) cc_final: 0.7315 (m) REVERT: E 92 LYS cc_start: 0.8489 (tppp) cc_final: 0.8146 (ttmt) REVERT: E 109 LYS cc_start: 0.8232 (tptt) cc_final: 0.7773 (tttp) REVERT: E 124 ARG cc_start: 0.6585 (OUTLIER) cc_final: 0.6148 (mtm180) REVERT: E 170 ARG cc_start: 0.6900 (ptt-90) cc_final: 0.6044 (mtp85) REVERT: E 196 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7377 (ppp) REVERT: E 392 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7451 (pp20) REVERT: E 413 LYS cc_start: 0.8128 (ttmt) cc_final: 0.7885 (mttt) REVERT: F 139 ARG cc_start: 0.8023 (ttm-80) cc_final: 0.7642 (ttp80) REVERT: F 147 ASP cc_start: 0.7764 (m-30) cc_final: 0.7317 (p0) REVERT: F 302 ASN cc_start: 0.7715 (t0) cc_final: 0.7317 (t0) REVERT: F 327 ASN cc_start: 0.6671 (p0) cc_final: 0.6244 (p0) REVERT: F 333 LYS cc_start: 0.7577 (ttpp) cc_final: 0.7137 (ttmt) REVERT: F 347 GLU cc_start: 0.7371 (mp0) cc_final: 0.6948 (mm-30) REVERT: F 368 MET cc_start: 0.5592 (mtp) cc_final: 0.5292 (mtt) REVERT: F 397 GLU cc_start: 0.6953 (tp30) cc_final: 0.6107 (tm-30) REVERT: F 398 GLN cc_start: 0.7620 (mt0) cc_final: 0.6977 (mp-120) REVERT: F 407 ARG cc_start: 0.7103 (ttp-170) cc_final: 0.6564 (ttm170) REVERT: F 410 ASP cc_start: 0.5730 (t0) cc_final: 0.5465 (t0) REVERT: F 431 ILE cc_start: 0.7107 (OUTLIER) cc_final: 0.6706 (pt) outliers start: 82 outliers final: 29 residues processed: 359 average time/residue: 0.6777 time to fit residues: 275.9386 Evaluate side-chains 313 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 276 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 330 THR 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 128 MET Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 301 LYS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 431 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 2 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 175 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 200 ASN C 302 ASN D 200 ASN E 167 ASN E 200 ASN F 140 GLN F 200 ASN F 295 ASN F 359 GLN F 399 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.174534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.143343 restraints weight = 22303.019| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.13 r_work: 0.3441 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21368 Z= 0.130 Angle : 0.530 8.059 28966 Z= 0.283 Chirality : 0.041 0.207 3246 Planarity : 0.003 0.035 3599 Dihedral : 10.529 177.399 2941 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.42 % Allowed : 15.59 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.17), residues: 2580 helix: 1.74 (0.15), residues: 1355 sheet: 0.19 (0.30), residues: 332 loop : -1.35 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 236 TYR 0.014 0.001 TYR D 312 PHE 0.017 0.002 PHE D 65 TRP 0.012 0.001 TRP B 162 HIS 0.005 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (21368) covalent geometry : angle 0.52988 / 0.28 (28966) hydrogen bonds : bond 0.03421 / 2.30 ( 1056) hydrogen bonds : angle 4.58640 / 3.26 ( 3033) *********************** 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 394 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 295 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7939 (mtpm) REVERT: A 140 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7620 (mt0) REVERT: A 333 LYS cc_start: 0.7115 (OUTLIER) cc_final: 0.6767 (mmmt) REVERT: A 337 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7072 (mp0) REVERT: A 373 GLU cc_start: 0.3143 (OUTLIER) cc_final: 0.2920 (mt-10) REVERT: A 427 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7759 (ttpp) REVERT: B 92 LYS cc_start: 0.8641 (mmtt) cc_final: 0.8316 (mmtp) REVERT: B 96 LYS cc_start: 0.8549 (mtpp) cc_final: 0.8219 (mttt) REVERT: B 109 LYS cc_start: 0.8546 (ttmm) cc_final: 0.8330 (tttt) REVERT: B 200 ASN cc_start: 0.6342 (OUTLIER) cc_final: 0.6102 (m-40) REVERT: B 231 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8009 (mp0) REVERT: B 274 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7314 (mtm-85) REVERT: C 92 LYS cc_start: 0.8353 (mmmm) cc_final: 0.8036 (mppt) REVERT: C 128 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6488 (mtt) REVERT: C 313 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7020 (pt) REVERT: D 1 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8086 (ptm) REVERT: D 3 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7605 (mp0) REVERT: D 86 ASP cc_start: 0.7157 (OUTLIER) cc_final: 0.6126 (t70) REVERT: D 153 ASP cc_start: 0.7789 (t0) cc_final: 0.7216 (t70) REVERT: D 331 THR cc_start: 0.7617 (p) cc_final: 0.7296 (m) REVERT: D 384 MET cc_start: 0.9051 (mtp) cc_final: 0.8797 (mtt) REVERT: E 92 LYS cc_start: 0.8489 (tppp) cc_final: 0.8127 (ttmt) REVERT: E 109 LYS cc_start: 0.8264 (tptt) cc_final: 0.7794 (tttt) REVERT: E 124 ARG cc_start: 0.6505 (OUTLIER) cc_final: 0.6098 (mtm180) REVERT: E 170 ARG cc_start: 0.6928 (ptt-90) cc_final: 0.6012 (mtp85) REVERT: E 196 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7433 (ppp) REVERT: E 243 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7217 (m-30) REVERT: E 392 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7394 (pp20) REVERT: E 413 LYS cc_start: 0.8124 (ttmt) cc_final: 0.7849 (mttt) REVERT: F 139 ARG cc_start: 0.8035 (ttm-80) cc_final: 0.7582 (ttp80) REVERT: F 147 ASP cc_start: 0.7841 (m-30) cc_final: 0.7344 (p0) REVERT: F 184 LYS cc_start: 0.6739 (mmtp) cc_final: 0.6074 (mtpt) REVERT: F 302 ASN cc_start: 0.7687 (t0) cc_final: 0.7272 (t0) REVERT: F 327 ASN cc_start: 0.6665 (p0) cc_final: 0.6205 (p0) REVERT: F 333 LYS cc_start: 0.7585 (ttpp) cc_final: 0.7150 (ttmt) REVERT: F 347 GLU cc_start: 0.7420 (mp0) cc_final: 0.6960 (mm-30) REVERT: F 368 MET cc_start: 0.5558 (mtp) cc_final: 0.5260 (mtt) REVERT: F 397 GLU cc_start: 0.6943 (tp30) cc_final: 0.6075 (tm-30) REVERT: F 398 GLN cc_start: 0.7610 (mt0) cc_final: 0.6923 (mp-120) REVERT: F 407 ARG cc_start: 0.7210 (ttp-170) cc_final: 0.6537 (ttm170) REVERT: F 410 ASP cc_start: 0.5732 (t0) cc_final: 0.5520 (t0) REVERT: F 431 ILE cc_start: 0.7098 (OUTLIER) cc_final: 0.6724 (pt) outliers start: 99 outliers final: 42 residues processed: 365 average time/residue: 0.6599 time to fit residues: 273.4139 Evaluate side-chains 336 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 278 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 330 THR 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 50 VAL Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 301 LYS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 333 LYS Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 431 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 243 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 226 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 174 optimal weight: 0.3980 chunk 135 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 302 ASN D 100 GLN D 200 ASN E 167 ASN E 200 ASN F 140 GLN F 200 ASN F 295 ASN F 359 GLN F 399 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.173213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.142053 restraints weight = 22468.908| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.10 r_work: 0.3420 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21368 Z= 0.141 Angle : 0.542 9.673 28966 Z= 0.288 Chirality : 0.042 0.206 3246 Planarity : 0.003 0.034 3599 Dihedral : 10.600 176.458 2941 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.07 % Allowed : 16.18 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.17), residues: 2580 helix: 1.75 (0.15), residues: 1349 sheet: 0.20 (0.30), residues: 332 loop : -1.38 (0.19), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 139 TYR 0.012 0.001 TYR E 158 PHE 0.018 0.002 PHE D 65 TRP 0.012 0.001 TRP B 162 HIS 0.005 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (21368) covalent geometry : angle 0.54224 / 0.29 (28966) hydrogen bonds : bond 0.03438 / 2.32 ( 1056) hydrogen bonds : angle 4.59361 / 3.27 ( 3033) *********************** 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 385 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 294 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7927 (mtpm) REVERT: A 140 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7617 (mt0) REVERT: A 333 LYS cc_start: 0.7093 (OUTLIER) cc_final: 0.6789 (mmmt) REVERT: A 337 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6976 (mp0) REVERT: A 370 ASP cc_start: 0.6241 (m-30) cc_final: 0.5537 (t70) REVERT: A 373 GLU cc_start: 0.2998 (OUTLIER) cc_final: 0.2786 (mt-10) REVERT: A 411 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7247 (ttmm) REVERT: A 427 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7742 (ttpp) REVERT: B 92 LYS cc_start: 0.8648 (mmtt) cc_final: 0.8284 (mmtp) REVERT: B 96 LYS cc_start: 0.8551 (mtpp) cc_final: 0.8204 (mttt) REVERT: B 109 LYS cc_start: 0.8524 (ttmm) cc_final: 0.8295 (tttt) REVERT: B 231 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: B 274 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7338 (mtm-85) REVERT: C 92 LYS cc_start: 0.8374 (mmmm) cc_final: 0.8023 (mppt) REVERT: C 128 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6520 (mtt) REVERT: C 313 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.6956 (pt) REVERT: C 391 GLU cc_start: 0.7867 (mp0) cc_final: 0.7420 (mp0) REVERT: D 1 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8196 (ptm) REVERT: D 3 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7665 (mp0) REVERT: D 86 ASP cc_start: 0.7252 (OUTLIER) cc_final: 0.6165 (t70) REVERT: D 153 ASP cc_start: 0.7796 (t0) cc_final: 0.7202 (t70) REVERT: D 331 THR cc_start: 0.7610 (p) cc_final: 0.7293 (m) REVERT: D 384 MET cc_start: 0.9047 (mtp) cc_final: 0.8790 (mtt) REVERT: E 92 LYS cc_start: 0.8508 (tppp) cc_final: 0.8119 (ttmt) REVERT: E 109 LYS cc_start: 0.8309 (tptt) cc_final: 0.7802 (tttt) REVERT: E 124 ARG cc_start: 0.6483 (OUTLIER) cc_final: 0.6121 (mtm180) REVERT: E 170 ARG cc_start: 0.6912 (ptt-90) cc_final: 0.5974 (mtp85) REVERT: E 196 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7515 (ppp) REVERT: E 392 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7363 (pp20) REVERT: E 413 LYS cc_start: 0.8151 (ttmt) cc_final: 0.7866 (mttt) REVERT: F 139 ARG cc_start: 0.8015 (ttm-80) cc_final: 0.7519 (ttp80) REVERT: F 147 ASP cc_start: 0.7870 (m-30) cc_final: 0.7353 (p0) REVERT: F 184 LYS cc_start: 0.6692 (mmtp) cc_final: 0.6064 (mtpt) REVERT: F 302 ASN cc_start: 0.7618 (t0) cc_final: 0.7202 (t0) REVERT: F 327 ASN cc_start: 0.6701 (p0) cc_final: 0.6239 (p0) REVERT: F 333 LYS cc_start: 0.7566 (ttpp) cc_final: 0.7207 (ttmt) REVERT: F 347 GLU cc_start: 0.7433 (mp0) cc_final: 0.6942 (mm-30) REVERT: F 368 MET cc_start: 0.5554 (mtp) cc_final: 0.5275 (mtt) REVERT: F 384 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7756 (ttp) REVERT: F 397 GLU cc_start: 0.7000 (tp30) cc_final: 0.5992 (tm-30) REVERT: F 398 GLN cc_start: 0.7613 (mt0) cc_final: 0.6982 (mp-120) REVERT: F 407 ARG cc_start: 0.7263 (ttp-170) cc_final: 0.6612 (ttm170) REVERT: F 410 ASP cc_start: 0.5688 (t0) cc_final: 0.5451 (t0) REVERT: F 431 ILE cc_start: 0.7105 (OUTLIER) cc_final: 0.6727 (pt) outliers start: 91 outliers final: 47 residues processed: 351 average time/residue: 0.6787 time to fit residues: 270.3485 Evaluate side-chains 337 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 274 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 330 THR 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 50 VAL Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 301 LYS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 333 LYS Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 384 MET Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 431 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 221 optimal weight: 5.9990 chunk 85 optimal weight: 0.0050 chunk 99 optimal weight: 8.9990 chunk 62 optimal weight: 0.0980 chunk 6 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 227 optimal weight: 3.9990 chunk 243 optimal weight: 7.9990 chunk 253 optimal weight: 4.9990 chunk 223 optimal weight: 4.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 253 HIS C 302 ASN D 100 GLN D 200 ASN E 167 ASN E 200 ASN F 140 GLN F 200 ASN F 295 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.176196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.145574 restraints weight = 22509.557| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.10 r_work: 0.3475 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21368 Z= 0.106 Angle : 0.507 10.079 28966 Z= 0.271 Chirality : 0.040 0.205 3246 Planarity : 0.003 0.033 3599 Dihedral : 10.504 178.615 2941 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.40 % Allowed : 16.89 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.17), residues: 2580 helix: 1.90 (0.15), residues: 1349 sheet: 0.24 (0.30), residues: 332 loop : -1.39 (0.19), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 139 TYR 0.012 0.001 TYR C 158 PHE 0.013 0.001 PHE D 65 TRP 0.011 0.001 TRP F 89 HIS 0.005 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (21368) covalent geometry : angle 0.50740 / 0.27 (28966) hydrogen bonds : bond 0.03061 / 2.07 ( 1056) hydrogen bonds : angle 4.48008 / 3.19 ( 3033) *********************** 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 368 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 292 time to evaluate : 0.667 Fit side-chains REVERT: A 79 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7937 (mtpm) REVERT: A 140 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7623 (mt0) REVERT: A 258 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6818 (tp30) REVERT: A 333 LYS cc_start: 0.7059 (ttpt) cc_final: 0.6739 (mmmt) REVERT: A 337 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6945 (mp0) REVERT: A 370 ASP cc_start: 0.6191 (m-30) cc_final: 0.5523 (t70) REVERT: A 427 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7756 (ttpp) REVERT: B 92 LYS cc_start: 0.8620 (mmtt) cc_final: 0.8374 (mmtp) REVERT: B 96 LYS cc_start: 0.8541 (mtpp) cc_final: 0.8219 (mttt) REVERT: B 274 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7222 (mtm-85) REVERT: C 92 LYS cc_start: 0.8353 (mmmm) cc_final: 0.8050 (mppt) REVERT: C 128 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.6499 (mtt) REVERT: C 313 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.6966 (pt) REVERT: C 391 GLU cc_start: 0.7782 (mp0) cc_final: 0.7334 (mp0) REVERT: D 1 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8251 (ptm) REVERT: D 26 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: D 86 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6212 (t70) REVERT: D 120 PRO cc_start: 0.5572 (Cg_endo) cc_final: 0.5358 (Cg_exo) REVERT: D 153 ASP cc_start: 0.7746 (t0) cc_final: 0.7166 (t70) REVERT: D 331 THR cc_start: 0.7620 (p) cc_final: 0.7292 (m) REVERT: D 384 MET cc_start: 0.8980 (mtp) cc_final: 0.8765 (mtt) REVERT: E 92 LYS cc_start: 0.8465 (tppp) cc_final: 0.8103 (ttmt) REVERT: E 109 LYS cc_start: 0.8269 (tptt) cc_final: 0.7814 (tttt) REVERT: E 124 ARG cc_start: 0.6396 (OUTLIER) cc_final: 0.6140 (mtm180) REVERT: E 170 ARG cc_start: 0.6939 (ptt-90) cc_final: 0.6028 (mtp85) REVERT: E 196 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7479 (ppp) REVERT: E 243 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.7007 (m-30) REVERT: E 254 ILE cc_start: 0.8321 (tp) cc_final: 0.8110 (tt) REVERT: E 392 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7357 (pp20) REVERT: E 413 LYS cc_start: 0.8063 (ttmt) cc_final: 0.7841 (mttt) REVERT: F 139 ARG cc_start: 0.8091 (ttm-80) cc_final: 0.7635 (ttp80) REVERT: F 147 ASP cc_start: 0.7827 (m-30) cc_final: 0.7359 (p0) REVERT: F 184 LYS cc_start: 0.6719 (mmtp) cc_final: 0.6096 (mtpt) REVERT: F 302 ASN cc_start: 0.7596 (t0) cc_final: 0.7179 (t0) REVERT: F 327 ASN cc_start: 0.6584 (p0) cc_final: 0.6143 (p0) REVERT: F 333 LYS cc_start: 0.7608 (ttpp) cc_final: 0.7192 (ttmt) REVERT: F 347 GLU cc_start: 0.7408 (mp0) cc_final: 0.6967 (mm-30) REVERT: F 359 GLN cc_start: 0.6979 (pm20) cc_final: 0.6734 (pm20) REVERT: F 384 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7717 (ttp) REVERT: F 397 GLU cc_start: 0.7019 (tp30) cc_final: 0.6040 (tm-30) REVERT: F 398 GLN cc_start: 0.7430 (mt0) cc_final: 0.6902 (mp-120) REVERT: F 407 ARG cc_start: 0.7210 (ttp-170) cc_final: 0.6636 (ttm170) REVERT: F 431 ILE cc_start: 0.7048 (OUTLIER) cc_final: 0.6698 (pt) outliers start: 76 outliers final: 32 residues processed: 341 average time/residue: 0.6671 time to fit residues: 258.5130 Evaluate side-chains 317 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 271 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 330 THR 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 128 MET Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 384 MET Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 431 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 142 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 chunk 238 optimal weight: 10.0000 chunk 253 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 255 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 191 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 253 HIS C 302 ASN D 100 GLN D 140 GLN D 200 ASN E 167 ASN E 200 ASN F 140 GLN F 200 ASN F 295 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.168929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.137204 restraints weight = 22467.200| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.18 r_work: 0.3362 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 21368 Z= 0.283 Angle : 0.707 13.343 28966 Z= 0.367 Chirality : 0.048 0.236 3246 Planarity : 0.005 0.049 3599 Dihedral : 10.969 174.385 2941 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.84 % Allowed : 17.11 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.16), residues: 2580 helix: 1.23 (0.14), residues: 1352 sheet: 0.00 (0.29), residues: 341 loop : -1.37 (0.19), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 407 TYR 0.044 0.002 TYR C 312 PHE 0.029 0.003 PHE D 65 TRP 0.019 0.002 TRP B 162 HIS 0.007 0.002 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00672 / 0.28 (21368) covalent geometry : angle 0.70727 / 0.37 (28966) hydrogen bonds : bond 0.04419 / 2.97 ( 1056) hydrogen bonds : angle 4.93844 / 3.49 ( 3033) *********************** 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 366 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 280 time to evaluate : 0.812 Fit side-chains REVERT: A 79 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.8002 (mtpm) REVERT: A 136 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.6962 (t0) REVERT: A 140 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7584 (mt0) REVERT: A 333 LYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6908 (mmmt) REVERT: A 337 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7156 (mp0) REVERT: A 370 ASP cc_start: 0.6213 (m-30) cc_final: 0.5456 (t70) REVERT: A 427 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7939 (ttpp) REVERT: B 92 LYS cc_start: 0.8677 (mmtt) cc_final: 0.8445 (mmtp) REVERT: B 96 LYS cc_start: 0.8596 (mtpp) cc_final: 0.8262 (mttt) REVERT: B 128 MET cc_start: 0.6796 (OUTLIER) cc_final: 0.6559 (ttt) REVERT: B 231 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: B 274 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7329 (mtm-85) REVERT: C 92 LYS cc_start: 0.8370 (mmmm) cc_final: 0.8022 (mppt) REVERT: C 391 GLU cc_start: 0.7829 (mp0) cc_final: 0.7379 (mp0) REVERT: D 153 ASP cc_start: 0.7917 (t0) cc_final: 0.7581 (t0) REVERT: D 331 THR cc_start: 0.7752 (p) cc_final: 0.7453 (m) REVERT: D 429 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8568 (t) REVERT: E 92 LYS cc_start: 0.8612 (tppp) cc_final: 0.8220 (ttmt) REVERT: E 103 MET cc_start: 0.8374 (mmt) cc_final: 0.7614 (mtp) REVERT: E 109 LYS cc_start: 0.8423 (tptt) cc_final: 0.7846 (tttt) REVERT: E 170 ARG cc_start: 0.7098 (ptt-90) cc_final: 0.6035 (mtp85) REVERT: E 196 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7639 (ppp) REVERT: E 243 ASP cc_start: 0.7434 (m-30) cc_final: 0.7072 (m-30) REVERT: E 317 LYS cc_start: 0.7194 (OUTLIER) cc_final: 0.6437 (ptmt) REVERT: E 345 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6233 (tt0) REVERT: E 413 LYS cc_start: 0.8158 (ttmt) cc_final: 0.7856 (mttt) REVERT: F 147 ASP cc_start: 0.7924 (m-30) cc_final: 0.7409 (p0) REVERT: F 302 ASN cc_start: 0.7682 (t0) cc_final: 0.7227 (t0) REVERT: F 327 ASN cc_start: 0.6911 (p0) cc_final: 0.6448 (p0) REVERT: F 333 LYS cc_start: 0.7616 (ttpp) cc_final: 0.7212 (ttmt) REVERT: F 359 GLN cc_start: 0.7095 (pm20) cc_final: 0.6817 (pm20) REVERT: F 397 GLU cc_start: 0.6984 (tp30) cc_final: 0.6052 (tm-30) REVERT: F 398 GLN cc_start: 0.7583 (mt0) cc_final: 0.6964 (mp-120) REVERT: F 407 ARG cc_start: 0.7329 (ttp-170) cc_final: 0.6456 (ttm170) REVERT: F 431 ILE cc_start: 0.7232 (pp) cc_final: 0.6802 (pt) outliers start: 86 outliers final: 44 residues processed: 340 average time/residue: 0.6512 time to fit residues: 252.1595 Evaluate side-chains 311 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 256 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 301 LYS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 317 LYS Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 429 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 217 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 133 optimal weight: 0.2980 chunk 215 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS C 288 ASN C 302 ASN D 100 GLN D 140 GLN D 200 ASN E 167 ASN E 200 ASN F 140 GLN F 200 ASN F 295 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.173824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.142800 restraints weight = 22460.843| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.07 r_work: 0.3439 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3103 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= 0.122 Angle : 0.551 10.034 28966 Z= 0.291 Chirality : 0.041 0.213 3246 Planarity : 0.003 0.032 3599 Dihedral : 10.750 176.549 2941 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.28 % Allowed : 18.90 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.17), residues: 2580 helix: 1.63 (0.15), residues: 1351 sheet: 0.06 (0.29), residues: 334 loop : -1.33 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 139 TYR 0.022 0.001 TYR C 312 PHE 0.013 0.001 PHE D 65 TRP 0.013 0.001 TRP F 89 HIS 0.006 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (21368) covalent geometry : angle 0.55074 / 0.29 (28966) hydrogen bonds : bond 0.03304 / 2.23 ( 1056) hydrogen bonds : angle 4.62465 / 3.28 ( 3033) *********************** 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 328 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 277 time to evaluate : 0.888 Fit side-chains REVERT: A 79 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7919 (mtpm) REVERT: A 136 ASP cc_start: 0.7277 (OUTLIER) cc_final: 0.6829 (t0) REVERT: A 140 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7468 (mt0) REVERT: A 333 LYS cc_start: 0.7191 (ttpt) cc_final: 0.6869 (mmmm) REVERT: A 337 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7029 (mp0) REVERT: A 370 ASP cc_start: 0.6208 (m-30) cc_final: 0.5458 (t70) REVERT: A 427 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7889 (ttpp) REVERT: B 92 LYS cc_start: 0.8612 (mmtt) cc_final: 0.8346 (mmtp) REVERT: B 96 LYS cc_start: 0.8536 (mtpp) cc_final: 0.8206 (mttt) REVERT: B 103 MET cc_start: 0.8183 (mmt) cc_final: 0.7981 (tpt) REVERT: B 274 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7254 (mtm-85) REVERT: C 92 LYS cc_start: 0.8363 (mmmm) cc_final: 0.8039 (mppt) REVERT: C 391 GLU cc_start: 0.7767 (mp0) cc_final: 0.7334 (mp0) REVERT: D 1 MET cc_start: 0.8518 (ptp) cc_final: 0.8205 (ptm) REVERT: D 153 ASP cc_start: 0.7808 (t0) cc_final: 0.7227 (t70) REVERT: D 331 THR cc_start: 0.7634 (p) cc_final: 0.7334 (m) REVERT: D 429 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8501 (t) REVERT: E 92 LYS cc_start: 0.8546 (tppp) cc_final: 0.8169 (ttmt) REVERT: E 103 MET cc_start: 0.8258 (mmt) cc_final: 0.7660 (mtp) REVERT: E 109 LYS cc_start: 0.8311 (tptt) cc_final: 0.7896 (tptt) REVERT: E 124 ARG cc_start: 0.6480 (OUTLIER) cc_final: 0.6095 (mtm180) REVERT: E 170 ARG cc_start: 0.7070 (ptt-90) cc_final: 0.6073 (mtp180) REVERT: E 196 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7448 (ppp) REVERT: E 228 MET cc_start: 0.6289 (mmm) cc_final: 0.6077 (ptt) REVERT: E 243 ASP cc_start: 0.7371 (m-30) cc_final: 0.7025 (m-30) REVERT: E 254 ILE cc_start: 0.8335 (tp) cc_final: 0.8111 (tt) REVERT: E 317 LYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6270 (ptmt) REVERT: E 345 GLU cc_start: 0.6989 (tm-30) cc_final: 0.6229 (tt0) REVERT: E 413 LYS cc_start: 0.8076 (ttmt) cc_final: 0.7838 (mttp) REVERT: F 147 ASP cc_start: 0.7945 (m-30) cc_final: 0.7449 (p0) REVERT: F 327 ASN cc_start: 0.6806 (p0) cc_final: 0.6327 (p0) REVERT: F 333 LYS cc_start: 0.7610 (ttpp) cc_final: 0.7182 (ttmt) REVERT: F 359 GLN cc_start: 0.6992 (pm20) cc_final: 0.6692 (pm20) REVERT: F 384 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7519 (tpp) REVERT: F 397 GLU cc_start: 0.6973 (tp30) cc_final: 0.6073 (tm-30) REVERT: F 398 GLN cc_start: 0.7338 (mt0) cc_final: 0.6750 (mp-120) REVERT: F 407 ARG cc_start: 0.7204 (ttp-170) cc_final: 0.6573 (ttm170) outliers start: 51 outliers final: 26 residues processed: 310 average time/residue: 0.6841 time to fit residues: 239.7688 Evaluate side-chains 300 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 264 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 330 THR 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 319 CYS Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 317 LYS Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 384 MET Chi-restraints excluded: chain F residue 429 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 26 optimal weight: 0.0000 chunk 180 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 139 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN C 302 ASN D 62 ASN D 200 ASN D 279 GLN E 140 GLN E 167 ASN E 200 ASN F 140 GLN F 200 ASN F 295 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.175094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.144283 restraints weight = 22687.771| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.12 r_work: 0.3456 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21368 Z= 0.114 Angle : 0.537 12.896 28966 Z= 0.283 Chirality : 0.041 0.223 3246 Planarity : 0.003 0.034 3599 Dihedral : 10.592 175.038 2941 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.19 % Allowed : 19.08 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.17), residues: 2580 helix: 1.81 (0.15), residues: 1350 sheet: 0.04 (0.29), residues: 340 loop : -1.34 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 139 TYR 0.023 0.001 TYR A 312 PHE 0.014 0.001 PHE D 65 TRP 0.012 0.001 TRP E 154 HIS 0.005 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (21368) covalent geometry : angle 0.53659 / 0.28 (28966) hydrogen bonds : bond 0.03152 / 2.13 ( 1056) hydrogen bonds : angle 4.51266 / 3.20 ( 3033) ********************** 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 320 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 271 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7949 (mtpm) REVERT: A 140 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7623 (mt0) REVERT: A 246 LEU cc_start: 0.7677 (tp) cc_final: 0.7476 (mt) REVERT: A 265 LYS cc_start: 0.7581 (ttpp) cc_final: 0.7213 (tmtt) REVERT: A 333 LYS cc_start: 0.7134 (ttpt) cc_final: 0.6476 (mmmm) REVERT: A 337 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6987 (mp0) REVERT: A 369 SER cc_start: 0.6212 (OUTLIER) cc_final: 0.5973 (t) REVERT: A 370 ASP cc_start: 0.6149 (m-30) cc_final: 0.5444 (t70) REVERT: A 427 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7850 (ttpp) REVERT: B 92 LYS cc_start: 0.8617 (mmtt) cc_final: 0.8349 (mmtp) REVERT: B 96 LYS cc_start: 0.8561 (mtpp) cc_final: 0.8215 (mttt) REVERT: B 274 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7281 (mtm-85) REVERT: C 92 LYS cc_start: 0.8374 (mmmm) cc_final: 0.8053 (mppt) REVERT: C 391 GLU cc_start: 0.7751 (mp0) cc_final: 0.7317 (mp0) REVERT: D 1 MET cc_start: 0.8577 (ptp) cc_final: 0.8193 (ptm) REVERT: D 86 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.6316 (t70) REVERT: D 153 ASP cc_start: 0.7807 (t0) cc_final: 0.7506 (t0) REVERT: D 331 THR cc_start: 0.7642 (p) cc_final: 0.7321 (m) REVERT: D 384 MET cc_start: 0.8928 (mtp) cc_final: 0.8662 (mtt) REVERT: E 92 LYS cc_start: 0.8517 (tppp) cc_final: 0.8130 (ttmt) REVERT: E 103 MET cc_start: 0.8187 (mmt) cc_final: 0.7620 (mtp) REVERT: E 109 LYS cc_start: 0.8273 (tptt) cc_final: 0.7868 (tptt) REVERT: E 124 ARG cc_start: 0.6452 (OUTLIER) cc_final: 0.6101 (mtm180) REVERT: E 170 ARG cc_start: 0.7084 (ptt-90) cc_final: 0.6088 (mtp180) REVERT: E 243 ASP cc_start: 0.7204 (m-30) cc_final: 0.6877 (m-30) REVERT: E 254 ILE cc_start: 0.8314 (tp) cc_final: 0.8086 (tt) REVERT: E 345 GLU cc_start: 0.7020 (tm-30) cc_final: 0.6273 (tt0) REVERT: E 392 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7313 (pp20) REVERT: F 147 ASP cc_start: 0.7936 (m-30) cc_final: 0.7453 (p0) REVERT: F 302 ASN cc_start: 0.7588 (t0) cc_final: 0.7156 (t0) REVERT: F 327 ASN cc_start: 0.6737 (p0) cc_final: 0.6277 (p0) REVERT: F 333 LYS cc_start: 0.7629 (ttpp) cc_final: 0.7143 (ttmt) REVERT: F 359 GLN cc_start: 0.7004 (pm20) cc_final: 0.6675 (pm20) REVERT: F 384 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7706 (ttp) REVERT: F 397 GLU cc_start: 0.7022 (tp30) cc_final: 0.6141 (tm-30) REVERT: F 398 GLN cc_start: 0.7298 (mt0) cc_final: 0.6756 (mp-120) REVERT: F 407 ARG cc_start: 0.7219 (ttp-170) cc_final: 0.6302 (ttm170) outliers start: 49 outliers final: 26 residues processed: 304 average time/residue: 0.6725 time to fit residues: 232.4416 Evaluate side-chains 293 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 259 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 330 THR 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 319 CYS Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 384 MET Chi-restraints excluded: chain F residue 429 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 29 optimal weight: 0.9980 chunk 214 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 238 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 216 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 288 ASN C 302 ASN D 200 ASN E 140 GLN E 167 ASN E 200 ASN F 140 GLN F 200 ASN F 295 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.172042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.140690 restraints weight = 22461.555| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.12 r_work: 0.3408 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21368 Z= 0.172 Angle : 0.604 12.887 28966 Z= 0.314 Chirality : 0.043 0.223 3246 Planarity : 0.004 0.035 3599 Dihedral : 10.743 172.278 2941 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.59 % Allowed : 18.81 % 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 are not related in a simple way. whole: 0.64 (0.17), residues: 2580 helix: 1.63 (0.14), residues: 1350 sheet: 0.11 (0.30), residues: 325 loop : -1.33 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 139 TYR 0.025 0.002 TYR C 312 PHE 0.019 0.002 PHE D 65 TRP 0.018 0.001 TRP D 162 HIS 0.005 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (21368) covalent geometry : angle 0.60371 / 0.31 (28966) hydrogen bonds : bond 0.03595 / 2.43 ( 1056) hydrogen bonds : angle 4.67069 / 3.31 ( 3033) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8907.75 seconds wall clock time: 152 minutes 34.46 seconds (9154.46 seconds total)