Starting phenix.real_space_refine on Sun Sep 13 04:43:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dtp_27707/09_2026/8dtp_27707.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dtp_27707/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8dtp_27707/09_2026/8dtp_27707.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dtp_27707/09_2026/8dtp_27707.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dtp_27707/09_2026/8dtp_27707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dtp_27707/09_2026/8dtp_27707.map" model { file = "/net/cci-nas-00/data/ceres_data/8dtp_27707/09_2026/8dtp_27707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dtp_27707/09_2026/8dtp_27707.cif" } 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-2.2.1-6174/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: 4.89, per 1000 atoms: 0.23 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: 1.78 Conformation dependent library (CDL) restraints added in 979.7 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: 0.72 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: 3.75 Time building geometry restraints manager: 2.34 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: 1004 3.12 - 4.69: 143 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: 2.200 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.690 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.890 ------------------------------------------------------------------------------- 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= 0.306 Angle : 0.641 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 0.64066 / 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 : 0.802 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: 0.6895 time to fit residues: 445.9209 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 : 0.809 ------------------------------------------------------------------------------- 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 167 ASN F 62 ASN F 140 GLN F 200 ASN F 295 ASN F 359 GLN ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.174329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.144335 restraints weight = 23159.447| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.27 r_work: 0.3442 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 21368 Z= 0.197 Angle : 0.628 9.682 28966 Z= 0.334 Chirality : 0.045 0.228 3246 Planarity : 0.004 0.046 3599 Dihedral : 10.680 178.523 2950 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.38 % Allowed : 12.56 % Favored : 83.07 % 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: 0.43 (0.17), residues: 2580 helix: 1.39 (0.15), residues: 1348 sheet: -0.10 (0.29), residues: 351 loop : -1.28 (0.20), residues: 881 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 0.002 TRP A 162 HIS 0.006 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (21368) covalent geometry : angle 0.62802 / 0.33 (28966) hydrogen bonds : bond 0.04242 / 2.84 ( 1056) hydrogen bonds : angle 4.99483 / 3.56 ( 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 442 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 344 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 ASP cc_start: 0.7276 (m-30) cc_final: 0.7063 (t0) REVERT: A 333 LYS cc_start: 0.7088 (ttpt) cc_final: 0.6717 (mmmt) REVERT: A 337 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6916 (mp0) REVERT: B 49 SER cc_start: 0.8781 (t) cc_final: 0.8511 (p) REVERT: B 92 LYS cc_start: 0.8438 (mmtt) cc_final: 0.8181 (mmtp) REVERT: B 96 LYS cc_start: 0.8436 (mtpp) cc_final: 0.8156 (mttt) REVERT: B 109 LYS cc_start: 0.8394 (ttmm) cc_final: 0.8133 (tttt) REVERT: C 92 LYS cc_start: 0.8175 (mmmm) cc_final: 0.7949 (mppt) REVERT: C 101 ARG cc_start: 0.8523 (mmm160) cc_final: 0.8318 (mmm160) REVERT: C 184 LYS cc_start: 0.8511 (mtpp) cc_final: 0.8290 (mtpt) REVERT: D 26 GLU cc_start: 0.7537 (mp0) cc_final: 0.7297 (mm-30) REVERT: D 136 ASP cc_start: 0.7170 (t70) cc_final: 0.6955 (t0) REVERT: D 139 ARG cc_start: 0.7623 (ttp80) cc_final: 0.6924 (ttp-110) REVERT: D 153 ASP cc_start: 0.7667 (t0) cc_final: 0.7288 (t70) REVERT: D 226 MET cc_start: 0.8083 (mmm) cc_final: 0.7800 (mmm) REVERT: D 331 THR cc_start: 0.7684 (p) cc_final: 0.7334 (m) REVERT: D 389 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7478 (tp30) REVERT: E 92 LYS cc_start: 0.8424 (tppp) cc_final: 0.8164 (ttmt) REVERT: E 109 LYS cc_start: 0.8149 (tptt) cc_final: 0.7764 (tttm) REVERT: E 170 ARG cc_start: 0.6731 (ptt-90) cc_final: 0.6058 (mtp85) REVERT: E 196 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7175 (ppp) REVERT: E 317 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.6694 (ptmt) REVERT: E 340 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7042 (ttp80) REVERT: E 392 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7475 (pp20) REVERT: E 413 LYS cc_start: 0.8035 (ttmt) cc_final: 0.7827 (mttt) REVERT: F 139 ARG cc_start: 0.7903 (ttm-80) cc_final: 0.7680 (ttp80) REVERT: F 147 ASP cc_start: 0.7576 (m-30) cc_final: 0.7276 (p0) REVERT: F 247 ASP cc_start: 0.7242 (m-30) cc_final: 0.7004 (m-30) REVERT: F 302 ASN cc_start: 0.7713 (t0) cc_final: 0.7372 (t0) REVERT: F 327 ASN cc_start: 0.6926 (p0) cc_final: 0.6542 (p0) REVERT: F 333 LYS cc_start: 0.7609 (ttpp) cc_final: 0.7177 (ttmt) REVERT: F 347 GLU cc_start: 0.7224 (mp0) cc_final: 0.6965 (mm-30) REVERT: F 368 MET cc_start: 0.6007 (mtp) cc_final: 0.5761 (mtt) REVERT: F 397 GLU cc_start: 0.6828 (tp30) cc_final: 0.6231 (tm-30) REVERT: F 398 GLN cc_start: 0.7457 (mt0) cc_final: 0.6913 (mp-120) REVERT: F 407 ARG cc_start: 0.7085 (ttp-170) cc_final: 0.6432 (ttm170) REVERT: F 431 ILE cc_start: 0.7147 (pp) cc_final: 0.6659 (pt) outliers start: 98 outliers final: 29 residues processed: 410 average time/residue: 0.6463 time to fit residues: 299.8687 Evaluate side-chains 315 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 282 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 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 389 GLU 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 118 GLU 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 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: 0.5980 chunk 134 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 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: 1.9990 chunk 62 optimal weight: 0.6980 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.173537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.142370 restraints weight = 22369.360| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.17 r_work: 0.3428 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21368 Z= 0.150 Angle : 0.552 8.738 28966 Z= 0.297 Chirality : 0.042 0.231 3246 Planarity : 0.004 0.035 3599 Dihedral : 10.582 178.344 2942 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.38 % Allowed : 14.21 % Favored : 81.41 % 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: 0.56 (0.17), residues: 2580 helix: 1.54 (0.15), residues: 1350 sheet: 0.12 (0.30), residues: 334 loop : -1.35 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 177 TYR 0.015 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 B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (21368) covalent geometry : angle 0.55166 / 0.30 (28966) hydrogen bonds : bond 0.03859 / 2.59 ( 1056) hydrogen bonds : angle 4.79370 / 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 406 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 308 time to evaluate : 0.768 Fit side-chains REVERT: A 136 ASP cc_start: 0.7453 (m-30) cc_final: 0.7043 (t0) REVERT: A 258 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6869 (tp30) REVERT: A 333 LYS cc_start: 0.7067 (ttpt) cc_final: 0.6739 (mmmt) REVERT: A 337 GLU cc_start: 0.7468 (mt-10) cc_final: 0.6998 (mp0) REVERT: A 427 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7736 (ttpp) REVERT: B 92 LYS cc_start: 0.8589 (mmtt) cc_final: 0.8252 (mmtp) REVERT: B 96 LYS cc_start: 0.8558 (mtpp) cc_final: 0.8197 (mttt) REVERT: B 109 LYS cc_start: 0.8557 (ttmm) cc_final: 0.8294 (tttt) REVERT: C 92 LYS cc_start: 0.8349 (mmmm) cc_final: 0.8027 (mppt) REVERT: C 128 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.6547 (mtt) REVERT: D 1 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8164 (ptp) REVERT: D 3 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7570 (mp0) REVERT: D 26 GLU cc_start: 0.7727 (mp0) cc_final: 0.7462 (mp0) REVERT: D 86 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6184 (t70) REVERT: D 136 ASP cc_start: 0.7344 (t70) cc_final: 0.7139 (t0) REVERT: D 153 ASP cc_start: 0.7767 (t0) cc_final: 0.7233 (t70) REVERT: D 226 MET cc_start: 0.8197 (mmm) cc_final: 0.7980 (mmm) REVERT: D 331 THR cc_start: 0.7615 (p) cc_final: 0.7288 (m) REVERT: D 389 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7861 (tp30) REVERT: E 92 LYS cc_start: 0.8521 (tppp) cc_final: 0.8173 (ttmt) REVERT: E 109 LYS cc_start: 0.8266 (tptt) cc_final: 0.7801 (tttt) REVERT: E 170 ARG cc_start: 0.6865 (ptt-90) cc_final: 0.6041 (mtp85) REVERT: E 371 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7478 (pt) REVERT: E 392 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7438 (pp20) REVERT: E 413 LYS cc_start: 0.8147 (ttmt) cc_final: 0.7823 (mttt) REVERT: F 139 ARG cc_start: 0.7987 (ttm-80) cc_final: 0.7599 (ttp80) REVERT: F 147 ASP cc_start: 0.7765 (m-30) cc_final: 0.7295 (p0) REVERT: F 177 ARG cc_start: 0.6941 (mtm-85) cc_final: 0.6725 (mtm110) REVERT: F 302 ASN cc_start: 0.7730 (t0) cc_final: 0.7326 (t0) REVERT: F 327 ASN cc_start: 0.6736 (p0) cc_final: 0.6317 (p0) REVERT: F 333 LYS cc_start: 0.7618 (ttpp) cc_final: 0.7142 (ttmt) REVERT: F 347 GLU cc_start: 0.7353 (mp0) cc_final: 0.6944 (mm-30) REVERT: F 368 MET cc_start: 0.5662 (mtp) cc_final: 0.5322 (mtt) REVERT: F 397 GLU cc_start: 0.6979 (tp30) cc_final: 0.6152 (tm-30) REVERT: F 398 GLN cc_start: 0.7598 (mt0) cc_final: 0.6905 (mp-120) REVERT: F 407 ARG cc_start: 0.7170 (ttp-170) cc_final: 0.6454 (ttm170) REVERT: F 431 ILE cc_start: 0.7141 (pp) cc_final: 0.6686 (pt) outliers start: 98 outliers final: 36 residues processed: 378 average time/residue: 0.6518 time to fit residues: 279.2540 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 : 0.810 ------------------------------------------------------------------------------- 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 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 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 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 389 GLU 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 118 GLU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 304 VAL 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 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: 0.8980 chunk 237 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 201 optimal weight: 8.9990 chunk 219 optimal weight: 0.7980 chunk 250 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 E 200 ASN F 140 GLN F 200 ASN ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4059 r_free = 0.4059 target = 0.174493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.143273 restraints weight = 22475.735| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.08 r_work: 0.3440 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21368 Z= 0.127 Angle : 0.531 8.040 28966 Z= 0.284 Chirality : 0.041 0.225 3246 Planarity : 0.003 0.045 3599 Dihedral : 10.566 177.616 2942 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.11 % Allowed : 14.83 % Favored : 81.05 % 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: 0.65 (0.17), residues: 2580 helix: 1.63 (0.15), residues: 1355 sheet: 0.16 (0.30), residues: 334 loop : -1.37 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 139 TYR 0.024 0.001 TYR A 312 PHE 0.016 0.002 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 0.00279 / 0.13 (21368) covalent geometry : angle 0.53064 / 0.28 (28966) hydrogen bonds : bond 0.03498 / 2.35 ( 1056) hydrogen bonds : angle 4.64312 / 3.30 ( 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 393 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 301 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7938 (mtpm) REVERT: A 140 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7597 (mt0) REVERT: A 333 LYS cc_start: 0.7084 (ttpt) cc_final: 0.6817 (mmmt) REVERT: A 337 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7056 (mp0) REVERT: A 411 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7324 (ttmm) REVERT: B 92 LYS cc_start: 0.8607 (mmtt) cc_final: 0.8292 (mmtp) REVERT: B 96 LYS cc_start: 0.8551 (mtpp) cc_final: 0.8228 (mttt) REVERT: B 109 LYS cc_start: 0.8538 (ttmm) cc_final: 0.8325 (tttt) REVERT: B 200 ASN cc_start: 0.6338 (OUTLIER) cc_final: 0.5937 (m-40) REVERT: B 274 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7273 (mtm-85) REVERT: C 92 LYS cc_start: 0.8348 (mmmm) cc_final: 0.8023 (mppt) REVERT: C 128 MET cc_start: 0.6988 (OUTLIER) cc_final: 0.6501 (mtt) REVERT: D 1 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8121 (ptm) REVERT: D 3 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7616 (mp0) REVERT: D 86 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6124 (t70) REVERT: D 136 ASP cc_start: 0.7370 (t70) cc_final: 0.7156 (t0) REVERT: D 153 ASP cc_start: 0.7781 (t0) cc_final: 0.7223 (t70) REVERT: D 226 MET cc_start: 0.8189 (mmm) cc_final: 0.7948 (mmm) REVERT: D 331 THR cc_start: 0.7621 (p) cc_final: 0.7299 (m) REVERT: E 92 LYS cc_start: 0.8506 (tppp) cc_final: 0.8150 (ttmt) REVERT: E 109 LYS cc_start: 0.8249 (tptt) cc_final: 0.7785 (tttt) REVERT: E 124 ARG cc_start: 0.6430 (OUTLIER) cc_final: 0.6037 (mtm180) REVERT: E 170 ARG cc_start: 0.6899 (ptt-90) cc_final: 0.6044 (mtp85) REVERT: E 196 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7374 (ppp) REVERT: E 243 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7364 (m-30) REVERT: E 269 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7663 (mptm) REVERT: E 371 ILE cc_start: 0.7622 (OUTLIER) cc_final: 0.7375 (pt) REVERT: E 392 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7447 (pp20) REVERT: E 413 LYS cc_start: 0.8123 (ttmt) cc_final: 0.7858 (mttt) REVERT: F 139 ARG cc_start: 0.8020 (ttm-80) cc_final: 0.7637 (ttp80) REVERT: F 147 ASP cc_start: 0.7810 (m-30) cc_final: 0.7338 (p0) REVERT: F 302 ASN cc_start: 0.7723 (t0) cc_final: 0.7304 (t0) REVERT: F 327 ASN cc_start: 0.6676 (p0) cc_final: 0.6243 (p0) REVERT: F 333 LYS cc_start: 0.7582 (ttpp) cc_final: 0.7140 (ttmt) REVERT: F 347 GLU cc_start: 0.7422 (mp0) cc_final: 0.6972 (mm-30) REVERT: F 368 MET cc_start: 0.5628 (mtp) cc_final: 0.5324 (mtt) REVERT: F 397 GLU cc_start: 0.6937 (tp30) cc_final: 0.6101 (tm-30) REVERT: F 398 GLN cc_start: 0.7601 (mt0) cc_final: 0.6932 (mp10) REVERT: F 407 ARG cc_start: 0.7162 (ttp-170) cc_final: 0.6481 (ttm170) REVERT: F 431 ILE cc_start: 0.7114 (OUTLIER) cc_final: 0.6705 (pt) outliers start: 92 outliers final: 34 residues processed: 366 average time/residue: 0.6490 time to fit residues: 268.7747 Evaluate side-chains 322 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 274 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 411 LYS Chi-restraints excluded: chain A residue 418 LEU 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 274 ARG 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 304 VAL 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 76 LEU Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 118 GLU 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 269 LYS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 66 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 2 optimal weight: 7.9990 chunk 55 optimal weight: 0.4980 chunk 157 optimal weight: 3.9990 chunk 175 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 188 optimal weight: 0.0470 chunk 39 optimal weight: 10.0000 chunk 79 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.8282 ------------------------------------------------------------------------------- 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 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 ASN F 359 GLN F 399 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.172671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.141324 restraints weight = 22327.426| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.14 r_work: 0.3415 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21368 Z= 0.159 Angle : 0.559 9.015 28966 Z= 0.297 Chirality : 0.042 0.229 3246 Planarity : 0.004 0.035 3599 Dihedral : 10.667 175.338 2941 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.51 % Allowed : 15.33 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.17), residues: 2580 helix: 1.59 (0.15), residues: 1356 sheet: 0.16 (0.29), residues: 334 loop : -1.38 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 236 TYR 0.014 0.001 TYR D 312 PHE 0.019 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 0.00366 / 0.16 (21368) covalent geometry : angle 0.55931 / 0.30 (28966) hydrogen bonds : bond 0.03663 / 2.47 ( 1056) hydrogen bonds : angle 4.68502 / 3.33 ( 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 384 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 283 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7973 (mtpm) REVERT: A 140 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7607 (mt0) REVERT: A 203 LYS cc_start: 0.8081 (mtmm) cc_final: 0.7844 (mtmt) REVERT: A 333 LYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6836 (mmmt) REVERT: A 337 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7162 (mp0) REVERT: A 411 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7336 (ttmm) REVERT: A 427 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7775 (ttpp) REVERT: B 92 LYS cc_start: 0.8660 (mmtt) cc_final: 0.8424 (mmtp) REVERT: B 96 LYS cc_start: 0.8558 (mtpp) cc_final: 0.8233 (mttt) REVERT: B 109 LYS cc_start: 0.8569 (ttmm) cc_final: 0.8345 (tttt) REVERT: B 231 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8038 (mp0) REVERT: B 274 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7280 (mtm-85) REVERT: C 92 LYS cc_start: 0.8354 (mmmm) cc_final: 0.8035 (mppt) REVERT: C 128 MET cc_start: 0.7025 (OUTLIER) cc_final: 0.6500 (mtt) REVERT: D 3 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7674 (mp0) REVERT: D 136 ASP cc_start: 0.7379 (t70) cc_final: 0.7172 (t0) REVERT: D 153 ASP cc_start: 0.7816 (t0) cc_final: 0.7256 (t70) REVERT: D 331 THR cc_start: 0.7654 (p) cc_final: 0.7340 (m) REVERT: D 384 MET cc_start: 0.9040 (mtp) cc_final: 0.8776 (mtt) REVERT: D 389 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7909 (tp30) REVERT: E 92 LYS cc_start: 0.8527 (tppp) cc_final: 0.8164 (ttmt) REVERT: E 109 LYS cc_start: 0.8287 (tptt) cc_final: 0.7804 (tttt) REVERT: E 124 ARG cc_start: 0.6464 (OUTLIER) cc_final: 0.6091 (mtm180) REVERT: E 170 ARG cc_start: 0.7000 (ptt-90) cc_final: 0.6049 (mtp85) REVERT: E 196 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7488 (ppp) REVERT: E 317 LYS cc_start: 0.7037 (OUTLIER) cc_final: 0.6408 (ptmt) REVERT: E 371 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7521 (pt) REVERT: E 389 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7288 (tt0) REVERT: E 392 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7422 (pp20) REVERT: E 413 LYS cc_start: 0.8204 (ttmt) cc_final: 0.7904 (mttt) REVERT: F 139 ARG cc_start: 0.8018 (ttm-80) cc_final: 0.7566 (ttp80) REVERT: F 147 ASP cc_start: 0.7914 (m-30) cc_final: 0.7407 (p0) REVERT: F 184 LYS cc_start: 0.6696 (mmtp) cc_final: 0.6036 (mtpt) REVERT: F 302 ASN cc_start: 0.7728 (t0) cc_final: 0.7315 (t0) REVERT: F 327 ASN cc_start: 0.6843 (p0) cc_final: 0.6419 (p0) REVERT: F 333 LYS cc_start: 0.7671 (ttpp) cc_final: 0.7235 (ttmt) REVERT: F 347 GLU cc_start: 0.7454 (mp0) cc_final: 0.6980 (mm-30) REVERT: F 368 MET cc_start: 0.5623 (mtp) cc_final: 0.5302 (mtt) REVERT: F 397 GLU cc_start: 0.7015 (tp30) cc_final: 0.6016 (tm-30) REVERT: F 398 GLN cc_start: 0.7631 (mt0) cc_final: 0.6943 (mp-120) REVERT: F 407 ARG cc_start: 0.7273 (ttp-170) cc_final: 0.6518 (ttm170) REVERT: F 431 ILE cc_start: 0.7142 (OUTLIER) cc_final: 0.6755 (pt) outliers start: 101 outliers final: 45 residues processed: 352 average time/residue: 0.6712 time to fit residues: 266.7868 Evaluate side-chains 331 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 271 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 411 LYS 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 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 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 389 GLU 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 118 GLU Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 317 LYS 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 389 GLU 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 157 ASP 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: 5.9990 chunk 166 optimal weight: 4.9990 chunk 175 optimal weight: 7.9990 chunk 226 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 chunk 227 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 179 optimal weight: 0.0570 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- 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 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 ASN F 359 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.175195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.144639 restraints weight = 22446.789| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.16 r_work: 0.3443 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21368 Z= 0.111 Angle : 0.513 8.811 28966 Z= 0.274 Chirality : 0.041 0.226 3246 Planarity : 0.003 0.034 3599 Dihedral : 10.559 177.680 2941 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.53 % Allowed : 16.62 % Favored : 79.85 % 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: 0.77 (0.17), residues: 2580 helix: 1.76 (0.15), residues: 1357 sheet: 0.18 (0.29), residues: 336 loop : -1.36 (0.19), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 139 TYR 0.012 0.001 TYR F 149 PHE 0.014 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 0.00237 / 0.11 (21368) covalent geometry : angle 0.51335 / 0.27 (28966) hydrogen bonds : bond 0.03185 / 2.15 ( 1056) hydrogen bonds : angle 4.54215 / 3.23 ( 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 368 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 289 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7948 (mtpm) REVERT: A 140 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7609 (mt0) REVERT: A 333 LYS cc_start: 0.7194 (OUTLIER) cc_final: 0.6936 (mmmt) REVERT: A 337 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7104 (mp0) REVERT: A 370 ASP cc_start: 0.6314 (m-30) cc_final: 0.5621 (t70) REVERT: A 427 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7768 (ttpp) REVERT: B 92 LYS cc_start: 0.8645 (mmtt) cc_final: 0.8302 (mmtp) REVERT: B 96 LYS cc_start: 0.8554 (mtpp) cc_final: 0.8223 (mttt) REVERT: B 274 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7236 (mtm-85) REVERT: C 92 LYS cc_start: 0.8375 (mmmm) cc_final: 0.8059 (mppt) REVERT: C 128 MET cc_start: 0.6951 (OUTLIER) cc_final: 0.6496 (mtt) REVERT: C 313 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7001 (pt) REVERT: C 391 GLU cc_start: 0.7874 (mp0) cc_final: 0.7445 (mp0) REVERT: D 1 MET cc_start: 0.8506 (ptp) cc_final: 0.8214 (ptm) REVERT: D 3 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7667 (mp0) REVERT: D 136 ASP cc_start: 0.7387 (t70) cc_final: 0.7181 (t0) REVERT: D 153 ASP cc_start: 0.7787 (t0) cc_final: 0.7211 (t70) REVERT: D 331 THR cc_start: 0.7657 (p) cc_final: 0.7351 (m) REVERT: D 384 MET cc_start: 0.9025 (mtp) cc_final: 0.8792 (mtt) REVERT: E 92 LYS cc_start: 0.8493 (tppp) cc_final: 0.8128 (ttmt) REVERT: E 109 LYS cc_start: 0.8285 (tptt) cc_final: 0.7816 (tttt) REVERT: E 124 ARG cc_start: 0.6396 (OUTLIER) cc_final: 0.6117 (mtm180) REVERT: E 170 ARG cc_start: 0.6987 (ptt-90) cc_final: 0.6047 (mtp180) REVERT: E 196 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7493 (ppp) REVERT: E 243 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7127 (m-30) REVERT: E 333 LYS cc_start: 0.7046 (OUTLIER) cc_final: 0.6812 (mtpp) REVERT: E 392 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7361 (pp20) REVERT: E 413 LYS cc_start: 0.8120 (ttmt) cc_final: 0.7866 (mttt) REVERT: F 139 ARG cc_start: 0.8086 (ttm-80) cc_final: 0.7615 (ttp80) REVERT: F 147 ASP cc_start: 0.7913 (m-30) cc_final: 0.7390 (p0) REVERT: F 184 LYS cc_start: 0.6706 (mmtp) cc_final: 0.6054 (mtpt) REVERT: F 327 ASN cc_start: 0.6765 (p0) cc_final: 0.6320 (p0) REVERT: F 333 LYS cc_start: 0.7629 (ttpp) cc_final: 0.7277 (ttmt) REVERT: F 347 GLU cc_start: 0.7445 (mp0) cc_final: 0.6974 (mm-30) REVERT: F 397 GLU cc_start: 0.7040 (tp30) cc_final: 0.6029 (tm-30) REVERT: F 398 GLN cc_start: 0.7574 (mt0) cc_final: 0.6971 (mp-120) REVERT: F 407 ARG cc_start: 0.7247 (ttp-170) cc_final: 0.6625 (ttm170) REVERT: F 431 ILE cc_start: 0.7098 (OUTLIER) cc_final: 0.6737 (pt) outliers start: 79 outliers final: 37 residues processed: 348 average time/residue: 0.6237 time to fit residues: 246.0695 Evaluate side-chains 315 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 266 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 24 ASP 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 418 LEU Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 196 MET 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 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 71 SER 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 118 GLU 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 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 F residue 19 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 221 optimal weight: 0.0770 chunk 85 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 143 optimal weight: 0.2980 chunk 227 optimal weight: 4.9990 chunk 243 optimal weight: 4.9990 chunk 253 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.176148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.145243 restraints weight = 22557.490| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.09 r_work: 0.3473 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2891 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= 0.106 Angle : 0.511 11.299 28966 Z= 0.272 Chirality : 0.041 0.249 3246 Planarity : 0.003 0.033 3599 Dihedral : 10.479 177.595 2941 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.35 % Allowed : 16.89 % 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: 0.89 (0.17), residues: 2580 helix: 1.88 (0.15), residues: 1355 sheet: 0.31 (0.30), residues: 326 loop : -1.37 (0.19), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 101 TYR 0.023 0.001 TYR D 312 PHE 0.013 0.001 PHE D 65 TRP 0.010 0.001 TRP F 428 HIS 0.005 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (21368) covalent geometry : angle 0.51146 / 0.27 (28966) hydrogen bonds : bond 0.03065 / 2.07 ( 1056) hydrogen bonds : angle 4.47151 / 3.18 ( 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 360 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 285 time to evaluate : 0.827 Fit side-chains REVERT: A 79 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7944 (mtpm) REVERT: A 140 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7608 (mt0) REVERT: A 333 LYS cc_start: 0.7187 (OUTLIER) cc_final: 0.6917 (mmmt) REVERT: A 337 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7078 (mp0) REVERT: A 369 SER cc_start: 0.6063 (OUTLIER) cc_final: 0.5735 (t) REVERT: A 370 ASP cc_start: 0.6273 (m-30) cc_final: 0.5593 (t70) REVERT: A 427 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7736 (ttpp) REVERT: B 92 LYS cc_start: 0.8633 (mmtt) cc_final: 0.8371 (mmtp) REVERT: B 96 LYS cc_start: 0.8529 (mtpp) cc_final: 0.8203 (mttt) REVERT: B 231 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: B 274 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7253 (mtm-85) REVERT: C 92 LYS cc_start: 0.8364 (mmmm) cc_final: 0.8055 (mppt) REVERT: C 128 MET cc_start: 0.6986 (OUTLIER) cc_final: 0.6482 (mtt) REVERT: C 313 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7060 (pt) REVERT: C 391 GLU cc_start: 0.7781 (mp0) cc_final: 0.7326 (mp0) REVERT: D 1 MET cc_start: 0.8499 (ptp) cc_final: 0.8166 (ptm) REVERT: D 86 ASP cc_start: 0.7188 (OUTLIER) cc_final: 0.6207 (t70) REVERT: D 120 PRO cc_start: 0.5534 (Cg_endo) cc_final: 0.5325 (Cg_exo) REVERT: D 153 ASP cc_start: 0.7730 (t0) cc_final: 0.7141 (t70) REVERT: D 331 THR cc_start: 0.7625 (p) cc_final: 0.7305 (m) REVERT: D 384 MET cc_start: 0.8968 (mtp) cc_final: 0.8751 (mtt) REVERT: D 404 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8080 (mp) REVERT: E 92 LYS cc_start: 0.8463 (tppp) cc_final: 0.8096 (ttmt) REVERT: E 103 MET cc_start: 0.8250 (mmt) cc_final: 0.7511 (mtp) REVERT: E 109 LYS cc_start: 0.8267 (tptt) cc_final: 0.7806 (tttt) REVERT: E 124 ARG cc_start: 0.6406 (OUTLIER) cc_final: 0.6160 (mtm180) REVERT: E 170 ARG cc_start: 0.6944 (ptt-90) cc_final: 0.6044 (mtp180) REVERT: E 196 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7440 (ppp) REVERT: E 243 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.6954 (m-30) REVERT: E 317 LYS cc_start: 0.6951 (OUTLIER) cc_final: 0.6338 (ptmt) REVERT: E 392 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7343 (pp20) REVERT: E 413 LYS cc_start: 0.8047 (ttmt) cc_final: 0.7820 (mttt) REVERT: F 139 ARG cc_start: 0.8066 (ttm-80) cc_final: 0.7605 (ttp80) REVERT: F 147 ASP cc_start: 0.7866 (m-30) cc_final: 0.7382 (p0) REVERT: F 184 LYS cc_start: 0.6731 (mmtp) cc_final: 0.6099 (mtpt) REVERT: F 302 ASN cc_start: 0.7565 (t0) cc_final: 0.7135 (t0) REVERT: F 327 ASN cc_start: 0.6626 (p0) cc_final: 0.6190 (p0) REVERT: F 333 LYS cc_start: 0.7631 (ttpp) cc_final: 0.7217 (ttmt) REVERT: F 347 GLU cc_start: 0.7385 (mp0) cc_final: 0.6944 (mm-30) REVERT: F 359 GLN cc_start: 0.6979 (pm20) cc_final: 0.6769 (pm20) REVERT: F 397 GLU cc_start: 0.7037 (tp30) cc_final: 0.6055 (tm-30) REVERT: F 398 GLN cc_start: 0.7381 (mt0) cc_final: 0.6857 (mp-120) REVERT: F 407 ARG cc_start: 0.7198 (ttp-170) cc_final: 0.6627 (ttm170) REVERT: F 431 ILE cc_start: 0.7064 (OUTLIER) cc_final: 0.6715 (pt) outliers start: 75 outliers final: 35 residues processed: 336 average time/residue: 0.6433 time to fit residues: 244.9134 Evaluate side-chains 321 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 270 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 418 LEU Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain B residue 19 VAL 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 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 326 GLU Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 113 ILE 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 404 ILE 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 100 GLN Chi-restraints excluded: chain E residue 118 GLU 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 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 F residue 19 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 142 optimal weight: 9.9990 chunk 209 optimal weight: 4.9990 chunk 238 optimal weight: 3.9990 chunk 253 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 255 optimal weight: 8.9990 chunk 180 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 191 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 57 ASN B 253 HIS C 302 ASN 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 = 0.3980 r_free = 0.3980 target = 0.167417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.136401 restraints weight = 22512.661| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.07 r_work: 0.3327 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 21368 Z= 0.339 Angle : 0.761 12.063 28966 Z= 0.394 Chirality : 0.051 0.253 3246 Planarity : 0.005 0.055 3599 Dihedral : 11.103 174.395 2941 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.29 % Allowed : 16.71 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.16), residues: 2580 helix: 0.98 (0.14), residues: 1361 sheet: -0.08 (0.29), residues: 343 loop : -1.39 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 407 TYR 0.043 0.003 TYR C 312 PHE 0.031 0.003 PHE D 65 TRP 0.018 0.002 TRP E 154 HIS 0.008 0.002 HIS E 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00810 / 0.34 (21368) covalent geometry : angle 0.76081 / 0.39 (28966) hydrogen bonds : bond 0.04732 / 3.17 ( 1056) hydrogen bonds : angle 5.06088 / 3.58 ( 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 370 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 274 time to evaluate : 0.822 Fit side-chains REVERT: A 79 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8022 (mtpm) REVERT: A 136 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.6968 (t0) REVERT: A 140 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7612 (mt0) REVERT: A 333 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6937 (mmmt) REVERT: A 337 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7294 (mp0) REVERT: A 370 ASP cc_start: 0.6237 (m-30) cc_final: 0.5482 (t70) REVERT: A 427 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7966 (ttpp) REVERT: B 96 LYS cc_start: 0.8657 (mtpp) cc_final: 0.8386 (mttm) REVERT: B 231 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8082 (mp0) REVERT: B 274 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.7321 (mtm-85) REVERT: C 92 LYS cc_start: 0.8387 (mmmm) cc_final: 0.8046 (mppt) REVERT: C 128 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6570 (mtt) REVERT: C 391 GLU cc_start: 0.7861 (mp0) cc_final: 0.7406 (mp0) REVERT: D 139 ARG cc_start: 0.7883 (ttp80) cc_final: 0.7648 (ttp80) REVERT: D 153 ASP cc_start: 0.7987 (t0) cc_final: 0.7659 (t0) REVERT: D 331 THR cc_start: 0.7803 (p) cc_final: 0.7520 (m) REVERT: D 389 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7916 (tp30) REVERT: D 429 VAL cc_start: 0.8985 (OUTLIER) cc_final: 0.8618 (t) REVERT: E 92 LYS cc_start: 0.8669 (tppp) cc_final: 0.8288 (ttmt) REVERT: E 103 MET cc_start: 0.8533 (mmt) cc_final: 0.7943 (mtp) REVERT: E 159 GLU cc_start: 0.6783 (mp0) cc_final: 0.6232 (mp0) REVERT: E 170 ARG cc_start: 0.7123 (ptt-90) cc_final: 0.6053 (mtp180) REVERT: E 196 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7703 (ppp) REVERT: E 243 ASP cc_start: 0.7516 (m-30) cc_final: 0.7159 (m-30) REVERT: E 279 GLN cc_start: 0.7148 (pt0) cc_final: 0.6152 (tp40) REVERT: E 317 LYS cc_start: 0.7282 (OUTLIER) cc_final: 0.6508 (ptmt) REVERT: E 413 LYS cc_start: 0.8197 (ttmt) cc_final: 0.7882 (mttt) REVERT: F 123 LYS cc_start: 0.7045 (tmtm) cc_final: 0.6827 (ttmt) REVERT: F 139 ARG cc_start: 0.8110 (ttm-80) cc_final: 0.7678 (ttp80) REVERT: F 147 ASP cc_start: 0.8030 (m-30) cc_final: 0.7467 (p0) REVERT: F 327 ASN cc_start: 0.7082 (p0) cc_final: 0.6620 (p0) REVERT: F 333 LYS cc_start: 0.7674 (ttpp) cc_final: 0.7270 (ttmt) REVERT: F 347 GLU cc_start: 0.7461 (mp0) cc_final: 0.7258 (mp0) REVERT: F 397 GLU cc_start: 0.6968 (tp30) cc_final: 0.6040 (tm-30) REVERT: F 398 GLN cc_start: 0.7601 (mt0) cc_final: 0.6980 (mp-120) REVERT: F 431 ILE cc_start: 0.7314 (pp) cc_final: 0.6874 (pt) outliers start: 96 outliers final: 46 residues processed: 339 average time/residue: 0.5959 time to fit residues: 229.9879 Evaluate side-chains 318 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 260 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 356 VAL 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 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 B residue 366 VAL Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain C residue 19 VAL 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 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 306 THR Chi-restraints excluded: chain D residue 389 GLU 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 118 GLU 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 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 418 LEU 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: 0.0980 chunk 194 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 217 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 92 optimal weight: 0.0770 chunk 131 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 288 ASN C 302 ASN D 100 GLN D 200 ASN E 167 ASN E 200 ASN F 200 ASN ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.173811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.143249 restraints weight = 22484.090| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.17 r_work: 0.3431 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3145 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= 0.117 Angle : 0.547 9.185 28966 Z= 0.292 Chirality : 0.041 0.229 3246 Planarity : 0.003 0.032 3599 Dihedral : 10.805 176.359 2941 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.41 % Allowed : 19.17 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.17), residues: 2580 helix: 1.59 (0.15), residues: 1351 sheet: 0.06 (0.29), residues: 334 loop : -1.35 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 139 TYR 0.022 0.001 TYR A 312 PHE 0.017 0.001 PHE A 417 TRP 0.014 0.001 TRP F 89 HIS 0.005 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (21368) covalent geometry : angle 0.54741 / 0.29 (28966) hydrogen bonds : bond 0.03307 / 2.23 ( 1056) hydrogen bonds : angle 4.64433 / 3.30 ( 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 335 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 281 time to evaluate : 0.862 Fit side-chains REVERT: A 79 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7926 (mtpm) REVERT: A 136 ASP cc_start: 0.7277 (OUTLIER) cc_final: 0.6836 (t0) REVERT: A 140 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7472 (mt0) REVERT: A 333 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6903 (mmmm) REVERT: A 337 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7086 (mp0) REVERT: A 370 ASP cc_start: 0.6118 (m-30) cc_final: 0.5385 (t70) REVERT: A 419 MET cc_start: 0.7812 (tpp) cc_final: 0.7529 (tpt) REVERT: A 427 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7887 (ttpp) REVERT: B 96 LYS cc_start: 0.8543 (mtpp) cc_final: 0.8213 (mttt) REVERT: B 274 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7228 (mtm-85) REVERT: C 23 MET cc_start: 0.8419 (tpt) cc_final: 0.8203 (mmp) REVERT: C 92 LYS cc_start: 0.8386 (mmmm) cc_final: 0.8057 (mppt) REVERT: C 128 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6496 (mtt) REVERT: C 391 GLU cc_start: 0.7768 (mp0) cc_final: 0.7325 (mp0) REVERT: D 1 MET cc_start: 0.8464 (ptp) cc_final: 0.8257 (ptm) REVERT: D 86 ASP cc_start: 0.7364 (OUTLIER) cc_final: 0.6293 (t70) REVERT: D 139 ARG cc_start: 0.7840 (ttp80) cc_final: 0.7598 (ttp80) REVERT: D 153 ASP cc_start: 0.7839 (t0) cc_final: 0.7279 (t70) REVERT: D 331 THR cc_start: 0.7628 (p) cc_final: 0.7337 (m) REVERT: D 389 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7888 (tp30) REVERT: D 429 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8531 (t) REVERT: E 92 LYS cc_start: 0.8605 (tppp) cc_final: 0.8185 (ttmt) REVERT: E 109 LYS cc_start: 0.8318 (tptt) cc_final: 0.7906 (tptt) REVERT: E 124 ARG cc_start: 0.6419 (OUTLIER) cc_final: 0.6082 (mtm180) REVERT: E 159 GLU cc_start: 0.6679 (mp0) cc_final: 0.6142 (mp0) REVERT: E 170 ARG cc_start: 0.7096 (ptt-90) cc_final: 0.6085 (mtp180) REVERT: E 243 ASP cc_start: 0.7504 (m-30) cc_final: 0.7100 (m-30) REVERT: E 345 GLU cc_start: 0.6869 (tm-30) cc_final: 0.6320 (tt0) REVERT: E 413 LYS cc_start: 0.8071 (ttmt) cc_final: 0.7842 (mttt) REVERT: F 147 ASP cc_start: 0.7968 (m-30) cc_final: 0.7447 (p0) REVERT: F 302 ASN cc_start: 0.7625 (t0) cc_final: 0.7187 (t0) REVERT: F 327 ASN cc_start: 0.6843 (p0) cc_final: 0.6347 (p0) REVERT: F 333 LYS cc_start: 0.7591 (ttpp) cc_final: 0.7162 (ttmt) REVERT: F 347 GLU cc_start: 0.7406 (mp0) cc_final: 0.6970 (mm-30) REVERT: F 359 GLN cc_start: 0.7005 (pm20) cc_final: 0.6736 (pm20) REVERT: F 397 GLU cc_start: 0.6977 (tp30) cc_final: 0.6071 (tm-30) REVERT: F 398 GLN cc_start: 0.7372 (mt0) cc_final: 0.6808 (mp-120) outliers start: 54 outliers final: 29 residues processed: 318 average time/residue: 0.6597 time to fit residues: 238.2867 Evaluate side-chains 303 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 263 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 88 SER Chi-restraints excluded: chain B residue 131 VAL 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 128 MET Chi-restraints excluded: chain C residue 243 ASP 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 113 ILE Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 389 GLU 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 118 GLU 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 F residue 66 THR Chi-restraints excluded: chain F residue 325 SER 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: 6.9990 chunk 68 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 180 optimal weight: 0.0060 chunk 137 optimal weight: 0.5980 chunk 139 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 253 HIS C 288 ASN C 302 ASN D 200 ASN D 279 GLN E 140 GLN E 167 ASN E 200 ASN F 140 GLN ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.175891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.145578 restraints weight = 22706.604| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.14 r_work: 0.3456 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3213 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= 0.108 Angle : 0.533 12.759 28966 Z= 0.283 Chirality : 0.041 0.229 3246 Planarity : 0.003 0.034 3599 Dihedral : 10.588 175.248 2941 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.10 % Allowed : 19.48 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.17), residues: 2580 helix: 1.84 (0.15), residues: 1348 sheet: 0.02 (0.29), residues: 340 loop : -1.35 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 177 TYR 0.017 0.001 TYR A 70 PHE 0.016 0.001 PHE A 417 TRP 0.012 0.001 TRP F 89 HIS 0.005 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (21368) covalent geometry : angle 0.53252 / 0.28 (28966) hydrogen bonds : bond 0.03061 / 2.07 ( 1056) hydrogen bonds : angle 4.48574 / 3.19 ( 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 319 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 272 time to evaluate : 0.777 Fit side-chains REVERT: A 79 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7949 (mtpm) REVERT: A 140 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7601 (mt0) REVERT: A 247 ASP cc_start: 0.7655 (p0) cc_final: 0.7407 (m-30) REVERT: A 333 LYS cc_start: 0.7219 (OUTLIER) cc_final: 0.6569 (mmmm) REVERT: A 337 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7047 (mp0) REVERT: A 369 SER cc_start: 0.6043 (OUTLIER) cc_final: 0.5812 (t) REVERT: A 370 ASP cc_start: 0.6196 (m-30) cc_final: 0.5470 (t70) REVERT: A 427 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7879 (ttpp) REVERT: B 96 LYS cc_start: 0.8569 (mtpp) cc_final: 0.8228 (mttt) REVERT: B 231 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7942 (mp0) REVERT: B 274 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7227 (mtm-85) REVERT: C 92 LYS cc_start: 0.8394 (mmmm) cc_final: 0.8061 (mppt) REVERT: D 1 MET cc_start: 0.8533 (ptp) cc_final: 0.8268 (ptm) REVERT: D 86 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.6301 (t70) REVERT: D 139 ARG cc_start: 0.7852 (ttp80) cc_final: 0.7638 (ttp80) REVERT: D 153 ASP cc_start: 0.7798 (t0) cc_final: 0.7473 (t0) REVERT: D 331 THR cc_start: 0.7655 (p) cc_final: 0.7335 (m) REVERT: E 92 LYS cc_start: 0.8506 (tppp) cc_final: 0.8137 (ttmt) REVERT: E 109 LYS cc_start: 0.8253 (tptt) cc_final: 0.7867 (tptt) REVERT: E 159 GLU cc_start: 0.6689 (mp0) cc_final: 0.6201 (mp0) REVERT: E 170 ARG cc_start: 0.7068 (ptt-90) cc_final: 0.6096 (mtp180) REVERT: E 243 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.7036 (m-30) REVERT: E 345 GLU cc_start: 0.6927 (tm-30) cc_final: 0.6394 (tt0) REVERT: E 392 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7323 (pp20) REVERT: F 147 ASP cc_start: 0.7981 (m-30) cc_final: 0.7474 (p0) REVERT: F 168 LYS cc_start: 0.7152 (mptm) cc_final: 0.6868 (mmpt) REVERT: F 302 ASN cc_start: 0.7558 (t0) cc_final: 0.7122 (t0) REVERT: F 327 ASN cc_start: 0.6804 (p0) cc_final: 0.6359 (p0) REVERT: F 333 LYS cc_start: 0.7667 (ttpp) cc_final: 0.7187 (ttmt) REVERT: F 347 GLU cc_start: 0.7443 (mp0) cc_final: 0.6981 (mm-30) REVERT: F 359 GLN cc_start: 0.7039 (pm20) cc_final: 0.6734 (pm20) REVERT: F 397 GLU cc_start: 0.7000 (tp30) cc_final: 0.6106 (tm-30) REVERT: F 398 GLN cc_start: 0.7443 (mt0) cc_final: 0.6904 (mp-120) outliers start: 47 outliers final: 25 residues processed: 307 average time/residue: 0.6478 time to fit residues: 225.7414 Evaluate side-chains 290 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 256 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 418 LEU Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain B residue 131 VAL 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 243 ASP 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 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 243 ASP 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 F residue 66 THR Chi-restraints excluded: chain F residue 325 SER 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: 5.9990 chunk 214 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 238 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 216 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 GLN C 302 ASN D 200 ASN E 140 GLN E 167 ASN E 200 ASN F 140 GLN ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.170840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.140059 restraints weight = 22460.073| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.12 r_work: 0.3377 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 21368 Z= 0.212 Angle : 0.638 12.793 28966 Z= 0.332 Chirality : 0.045 0.243 3246 Planarity : 0.004 0.036 3599 Dihedral : 10.822 172.134 2941 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.59 % Allowed : 19.03 % Favored : 78.37 % 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: 0.54 (0.17), residues: 2580 helix: 1.50 (0.14), residues: 1352 sheet: 0.05 (0.30), residues: 333 loop : -1.30 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 236 TYR 0.027 0.002 TYR C 312 PHE 0.022 0.002 PHE D 65 TRP 0.019 0.002 TRP D 162 HIS 0.005 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 (21368) covalent geometry : angle 0.63847 / 0.33 (28966) hydrogen bonds : bond 0.03846 / 2.58 ( 1056) hydrogen bonds : angle 4.74418 / 3.36 ( 3033) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8786.42 seconds wall clock time: 150 minutes 22.14 seconds (9022.14 seconds total)