Starting phenix.real_space_refine on Sun Aug 24 15:20:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dtp_27707/08_2025/8dtp_27707.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dtp_27707/08_2025/8dtp_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dtp_27707/08_2025/8dtp_27707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dtp_27707/08_2025/8dtp_27707.map" model { file = "/net/cci-nas-00/data/ceres_data/8dtp_27707/08_2025/8dtp_27707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dtp_27707/08_2025/8dtp_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20944 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "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: 4.66, per 1000 atoms: 0.22 Number of scatterers: 20944 At special positions: 0 Unit cell: (112.608, 134.136, 141.588, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 119 16.00 P 27 15.00 Mg 5 11.99 O 4080 8.00 N 3469 7.00 C 13244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 788.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4920 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 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: 3.31 Time building geometry restraints manager: 1.61 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=" N VAL A 323 " pdb=" CA VAL A 323 " ideal model delta sigma weight residual 1.457 1.494 -0.038 1.19e-02 7.06e+03 9.93e+00 ... (remaining 21363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 27833 1.56 - 3.12: 966 3.12 - 4.69: 141 4.69 - 6.25: 25 6.25 - 7.81: 1 Bond angle restraints: 28966 Sorted by residual: angle pdb=" N ASP A 82 " pdb=" CA ASP A 82 " pdb=" C ASP A 82 " ideal model delta sigma weight residual 112.57 108.09 4.48 1.13e+00 7.83e-01 1.57e+01 angle pdb=" CA PHE D 383 " pdb=" CB PHE D 383 " pdb=" CG PHE D 383 " ideal model delta sigma weight residual 113.80 117.73 -3.93 1.00e+00 1.00e+00 1.54e+01 angle pdb=" C GLY F 151 " pdb=" N HIS F 152 " pdb=" CA HIS F 152 " ideal model delta sigma weight residual 122.30 117.08 5.22 1.35e+00 5.49e-01 1.50e+01 angle pdb=" N ASP F 382 " pdb=" CA ASP F 382 " pdb=" C ASP F 382 " ideal model delta sigma weight residual 114.31 109.48 4.83 1.29e+00 6.01e-01 1.40e+01 angle pdb=" N GLU A 122 " pdb=" CA GLU A 122 " pdb=" C GLU A 122 " ideal model delta sigma weight residual 111.71 107.41 4.30 1.15e+00 7.56e-01 1.40e+01 ... (remaining 28961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 12753 35.65 - 71.31: 169 71.31 - 106.96: 4 106.96 - 142.61: 1 142.61 - 178.27: 4 Dihedral angle restraints: 12931 sinusoidal: 5317 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 12928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2404 0.044 - 0.088: 561 0.088 - 0.132: 237 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: 3.380 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 16.720 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 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= 0.292 Angle : 0.633 7.809 28966 Z= 0.424 Chirality : 0.046 0.219 3246 Planarity : 0.004 0.075 3599 Dihedral : 12.189 178.266 8011 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 aren 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 covalent geometry : bond 0.00421 (21368) covalent geometry : angle 0.63325 (28966) hydrogen bonds : bond 0.15695 ( 1056) hydrogen bonds : angle 6.38349 ( 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 : 0.696 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: 0.6476 time to fit residues: 418.1433 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 : 0.672 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 57 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.174468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.144506 restraints weight = 23116.776| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.17 r_work: 0.3460 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21368 Z= 0.199 Angle : 0.618 9.376 28966 Z= 0.328 Chirality : 0.044 0.221 3246 Planarity : 0.004 0.043 3599 Dihedral : 11.052 177.583 3005 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.24 % Allowed : 12.60 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.17), residues: 2580 helix: 1.45 (0.15), residues: 1347 sheet: -0.13 (0.29), residues: 353 loop : -1.26 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 322 TYR 0.017 0.002 TYR B 312 PHE 0.023 0.003 PHE D 65 TRP 0.013 0.002 TRP A 162 HIS 0.006 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00464 (21368) covalent geometry : angle 0.61844 (28966) hydrogen bonds : bond 0.04342 ( 1056) hydrogen bonds : angle 5.01768 ( 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 438 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 343 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 ASP cc_start: 0.7558 (m-30) cc_final: 0.7206 (t0) REVERT: A 333 LYS cc_start: 0.7135 (mtpt) cc_final: 0.6737 (mmmt) REVERT: A 337 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7076 (mp0) REVERT: A 414 TRP cc_start: 0.7445 (m100) cc_final: 0.7164 (m-90) REVERT: B 49 SER cc_start: 0.8825 (t) cc_final: 0.8519 (p) REVERT: B 92 LYS cc_start: 0.8646 (mmtt) cc_final: 0.8366 (mmtp) REVERT: B 96 LYS cc_start: 0.8561 (mtpp) cc_final: 0.8269 (mttt) REVERT: B 109 LYS cc_start: 0.8557 (ttmm) cc_final: 0.8273 (tttt) REVERT: C 18 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.7179 (tmtp) REVERT: C 92 LYS cc_start: 0.8351 (mmmm) cc_final: 0.8084 (mppt) REVERT: C 101 ARG cc_start: 0.8646 (mmm160) cc_final: 0.8436 (mmm160) REVERT: C 184 LYS cc_start: 0.8543 (mtpp) cc_final: 0.8298 (mtpt) REVERT: D 1 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8038 (ptp) REVERT: D 26 GLU cc_start: 0.7763 (mp0) cc_final: 0.7492 (mm-30) REVERT: D 136 ASP cc_start: 0.7301 (t70) cc_final: 0.7094 (t0) REVERT: D 139 ARG cc_start: 0.7769 (ttp80) cc_final: 0.7072 (ttp-110) REVERT: D 153 ASP cc_start: 0.7817 (t0) cc_final: 0.7408 (t70) REVERT: D 177 ARG cc_start: 0.8148 (mtm110) cc_final: 0.7906 (mtm-85) REVERT: D 226 MET cc_start: 0.8152 (mmm) cc_final: 0.7866 (mmm) REVERT: D 331 THR cc_start: 0.7756 (p) cc_final: 0.7377 (m) REVERT: E 92 LYS cc_start: 0.8564 (tppp) cc_final: 0.8288 (ttmt) REVERT: E 109 LYS cc_start: 0.8282 (tptt) cc_final: 0.7894 (tttm) REVERT: E 170 ARG cc_start: 0.6814 (ptt-90) cc_final: 0.6085 (mtp85) REVERT: E 196 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7379 (ppp) REVERT: E 317 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.6654 (ptmt) REVERT: E 340 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6525 (ttp80) REVERT: E 392 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7462 (pp20) REVERT: E 413 LYS cc_start: 0.8098 (ttmt) cc_final: 0.7842 (mttt) REVERT: F 139 ARG cc_start: 0.8056 (ttm-80) cc_final: 0.7727 (ttp80) REVERT: F 147 ASP cc_start: 0.7821 (m-30) cc_final: 0.7345 (p0) REVERT: F 243 ASP cc_start: 0.7487 (m-30) cc_final: 0.7275 (t0) REVERT: F 247 ASP cc_start: 0.7381 (m-30) cc_final: 0.7130 (m-30) REVERT: F 302 ASN cc_start: 0.7706 (t0) cc_final: 0.7343 (t0) REVERT: F 327 ASN cc_start: 0.6888 (p0) cc_final: 0.6505 (p0) REVERT: F 333 LYS cc_start: 0.7674 (ttpp) cc_final: 0.7247 (ttmt) REVERT: F 347 GLU cc_start: 0.7278 (mp0) cc_final: 0.6944 (mm-30) REVERT: F 368 MET cc_start: 0.6041 (mtp) cc_final: 0.5737 (mtt) REVERT: F 397 GLU cc_start: 0.6932 (tp30) cc_final: 0.6195 (tm-30) REVERT: F 398 GLN cc_start: 0.7534 (mt0) cc_final: 0.6915 (mp-120) REVERT: F 407 ARG cc_start: 0.7217 (ttp-170) cc_final: 0.6439 (ttm170) REVERT: F 431 ILE cc_start: 0.7136 (pp) cc_final: 0.6643 (pt) outliers start: 95 outliers final: 31 residues processed: 407 average time/residue: 0.6475 time to fit residues: 297.1980 Evaluate side-chains 317 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 281 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 18 LYS 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 326 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 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 E residue 401 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 321 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 147 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 252 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 14 optimal weight: 0.0770 chunk 176 optimal weight: 5.9990 chunk 258 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN B 200 ASN C 288 ASN C 302 ASN D 13 GLN D 100 GLN D 140 GLN D 200 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.172189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.141005 restraints weight = 22371.485| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.11 r_work: 0.3399 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2400 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= 0.171 Angle : 0.577 9.367 28966 Z= 0.309 Chirality : 0.043 0.217 3246 Planarity : 0.004 0.036 3599 Dihedral : 11.039 175.955 2997 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.92 % Allowed : 13.63 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.17), residues: 2580 helix: 1.46 (0.15), residues: 1355 sheet: 0.09 (0.30), residues: 334 loop : -1.38 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 177 TYR 0.018 0.001 TYR B 312 PHE 0.021 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 covalent geometry : bond 0.00395 (21368) covalent geometry : angle 0.57698 (28966) hydrogen bonds : bond 0.04003 ( 1056) hydrogen bonds : angle 4.84483 ( 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 418 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 308 time to evaluate : 0.752 Fit side-chains REVERT: A 79 LYS cc_start: 0.8325 (ttmp) cc_final: 0.8038 (mtpm) REVERT: A 136 ASP cc_start: 0.7445 (m-30) cc_final: 0.6991 (t0) REVERT: A 196 MET cc_start: 0.8572 (mmp) cc_final: 0.8314 (mmp) REVERT: A 333 LYS cc_start: 0.7048 (ttpt) cc_final: 0.6700 (mmmt) REVERT: A 337 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7038 (mp0) REVERT: A 411 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7351 (ttmm) REVERT: A 414 TRP cc_start: 0.7460 (m100) cc_final: 0.7174 (m-90) REVERT: A 427 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7730 (ttpp) REVERT: B 92 LYS cc_start: 0.8619 (mmtt) cc_final: 0.8312 (mmtp) REVERT: B 96 LYS cc_start: 0.8584 (mtpp) cc_final: 0.8232 (mttt) REVERT: B 109 LYS cc_start: 0.8562 (ttmm) cc_final: 0.8279 (tttt) REVERT: B 200 ASN cc_start: 0.6554 (OUTLIER) cc_final: 0.6340 (m-40) REVERT: B 274 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7325 (mtm-85) REVERT: C 18 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.7143 (tmtp) REVERT: C 92 LYS cc_start: 0.8359 (mmmm) cc_final: 0.8008 (mppt) REVERT: C 128 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6541 (mtt) REVERT: C 236 ARG cc_start: 0.8593 (mtt-85) cc_final: 0.8383 (mtp180) REVERT: C 313 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7190 (pp) REVERT: D 1 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8154 (ptm) REVERT: D 3 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7557 (mp0) REVERT: D 26 GLU cc_start: 0.7766 (mp0) cc_final: 0.7457 (mp0) REVERT: D 86 ASP cc_start: 0.7130 (OUTLIER) cc_final: 0.6149 (t70) REVERT: D 136 ASP cc_start: 0.7360 (t70) cc_final: 0.7146 (t0) REVERT: D 153 ASP cc_start: 0.7786 (t0) cc_final: 0.7237 (t70) REVERT: D 226 MET cc_start: 0.8200 (mmm) cc_final: 0.7976 (mmm) REVERT: D 331 THR cc_start: 0.7617 (p) cc_final: 0.7304 (m) REVERT: D 389 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7952 (tp30) REVERT: E 92 LYS cc_start: 0.8556 (tppp) cc_final: 0.8185 (ttmt) REVERT: E 109 LYS cc_start: 0.8286 (tptt) cc_final: 0.7791 (tttt) REVERT: E 124 ARG cc_start: 0.6578 (OUTLIER) cc_final: 0.6159 (mtm180) REVERT: E 170 ARG cc_start: 0.6879 (ptt-90) cc_final: 0.6030 (mtp85) REVERT: E 196 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7527 (ppp) REVERT: E 371 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7514 (pt) REVERT: E 392 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7420 (pp20) REVERT: E 413 LYS cc_start: 0.8186 (ttmt) cc_final: 0.7834 (mttt) REVERT: F 139 ARG cc_start: 0.7974 (ttm-80) cc_final: 0.7547 (ttp80) REVERT: F 147 ASP cc_start: 0.7765 (m-30) cc_final: 0.7282 (p0) REVERT: F 177 ARG cc_start: 0.6977 (mtm-85) cc_final: 0.6770 (mtm110) REVERT: F 243 ASP cc_start: 0.7631 (m-30) cc_final: 0.7297 (t0) REVERT: F 302 ASN cc_start: 0.7734 (t0) cc_final: 0.7329 (t0) REVERT: F 327 ASN cc_start: 0.6807 (p0) cc_final: 0.6386 (p0) REVERT: F 333 LYS cc_start: 0.7622 (ttpp) cc_final: 0.7164 (ttmt) REVERT: F 347 GLU cc_start: 0.7369 (mp0) cc_final: 0.6927 (mm-30) REVERT: F 370 ASP cc_start: 0.5985 (m-30) cc_final: 0.5773 (m-30) REVERT: F 397 GLU cc_start: 0.6986 (tp30) cc_final: 0.6155 (tm-30) REVERT: F 398 GLN cc_start: 0.7571 (mt0) cc_final: 0.6877 (mp-120) REVERT: F 407 ARG cc_start: 0.7174 (ttp-170) cc_final: 0.6428 (ttm170) REVERT: F 431 ILE cc_start: 0.7165 (pp) cc_final: 0.6705 (pt) outliers start: 110 outliers final: 41 residues processed: 390 average time/residue: 0.6221 time to fit residues: 273.3387 Evaluate side-chains 333 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 279 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 131 VAL 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 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 18 LYS 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 313 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 363 SER 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 115 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 148 SER 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 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 325 SER 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: 1.9990 chunk 97 optimal weight: 0.7980 chunk 237 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 201 optimal weight: 9.9990 chunk 219 optimal weight: 5.9990 chunk 250 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 ASN B 288 ASN C 302 ASN D 100 GLN D 140 GLN D 200 ASN E 167 ASN E 200 ASN F 140 GLN F 200 ASN F 295 ASN 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 = 0.4025 r_free = 0.4025 target = 0.171326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.139785 restraints weight = 22488.640| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.14 r_work: 0.3395 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21368 Z= 0.188 Angle : 0.597 9.831 28966 Z= 0.315 Chirality : 0.043 0.185 3246 Planarity : 0.004 0.040 3599 Dihedral : 11.158 173.123 2997 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.74 % Allowed : 14.08 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.17), residues: 2580 helix: 1.37 (0.15), residues: 1359 sheet: 0.11 (0.29), residues: 334 loop : -1.37 (0.19), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 139 TYR 0.017 0.001 TYR A 312 PHE 0.022 0.002 PHE D 65 TRP 0.014 0.001 TRP B 162 HIS 0.005 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00439 (21368) covalent geometry : angle 0.59670 (28966) hydrogen bonds : bond 0.03962 ( 1056) hydrogen bonds : angle 4.83020 ( 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: 106 poor density : 287 time to evaluate : 0.707 Fit side-chains REVERT: A 79 LYS cc_start: 0.8231 (ttmp) cc_final: 0.7952 (mtpm) REVERT: A 140 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7631 (mt0) REVERT: A 333 LYS cc_start: 0.7176 (OUTLIER) cc_final: 0.6844 (mmmt) REVERT: A 337 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7255 (mp0) REVERT: A 411 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7332 (ttmm) REVERT: A 414 TRP cc_start: 0.7495 (m100) cc_final: 0.7161 (m-90) REVERT: A 427 LYS cc_start: 0.8109 (ttpm) cc_final: 0.7813 (ttpp) REVERT: B 96 LYS cc_start: 0.8586 (mtpp) cc_final: 0.8315 (mttm) REVERT: B 109 LYS cc_start: 0.8568 (ttmm) cc_final: 0.8298 (tttt) REVERT: B 274 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7292 (mtm-85) REVERT: C 18 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.7167 (tmtp) REVERT: C 92 LYS cc_start: 0.8352 (mmmm) cc_final: 0.8020 (mppt) REVERT: C 128 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.6554 (mtt) REVERT: C 236 ARG cc_start: 0.8572 (mtt-85) cc_final: 0.8354 (mtp180) REVERT: C 313 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7247 (pp) REVERT: D 1 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8124 (ptm) REVERT: D 3 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7588 (mp0) REVERT: D 26 GLU cc_start: 0.7767 (mp0) cc_final: 0.7498 (mp0) REVERT: D 136 ASP cc_start: 0.7394 (t70) cc_final: 0.7133 (t70) REVERT: D 153 ASP cc_start: 0.7853 (t0) cc_final: 0.7318 (t70) REVERT: D 226 MET cc_start: 0.8206 (mmm) cc_final: 0.7977 (mmm) REVERT: D 331 THR cc_start: 0.7641 (p) cc_final: 0.7339 (m) REVERT: D 389 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7964 (tp30) REVERT: E 26 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7789 (mt-10) REVERT: E 92 LYS cc_start: 0.8581 (tppp) cc_final: 0.8189 (ttmt) REVERT: E 109 LYS cc_start: 0.8313 (tptt) cc_final: 0.7809 (tttt) REVERT: E 124 ARG cc_start: 0.6558 (OUTLIER) cc_final: 0.6114 (mtm180) REVERT: E 170 ARG cc_start: 0.6964 (ptt-90) cc_final: 0.6022 (mtp85) REVERT: E 196 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7570 (ppp) REVERT: E 243 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7372 (m-30) REVERT: E 317 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6529 (ptmt) REVERT: E 326 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6800 (mt-10) REVERT: E 371 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7643 (pt) REVERT: E 392 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7426 (pp20) REVERT: E 413 LYS cc_start: 0.8214 (ttmt) cc_final: 0.7901 (mttt) REVERT: F 139 ARG cc_start: 0.7978 (ttm-80) cc_final: 0.7656 (ttp80) REVERT: F 147 ASP cc_start: 0.7862 (m-30) cc_final: 0.7370 (p0) REVERT: F 184 LYS cc_start: 0.6658 (mmtp) cc_final: 0.6033 (mtpt) REVERT: F 243 ASP cc_start: 0.7632 (m-30) cc_final: 0.7161 (t0) REVERT: F 302 ASN cc_start: 0.7765 (t0) cc_final: 0.7347 (t0) REVERT: F 327 ASN cc_start: 0.6965 (p0) cc_final: 0.6547 (p0) REVERT: F 333 LYS cc_start: 0.7677 (ttpp) cc_final: 0.7218 (ttmt) REVERT: F 347 GLU cc_start: 0.7447 (mp0) cc_final: 0.6985 (mm-30) REVERT: F 368 MET cc_start: 0.5691 (mtp) cc_final: 0.5449 (mtt) REVERT: F 397 GLU cc_start: 0.6966 (tp30) cc_final: 0.5990 (tm-30) REVERT: F 398 GLN cc_start: 0.7613 (mt0) cc_final: 0.6878 (mp-120) REVERT: F 407 ARG cc_start: 0.7229 (ttp-170) cc_final: 0.6485 (ttm170) REVERT: F 431 ILE cc_start: 0.7166 (pp) cc_final: 0.6725 (pt) outliers start: 106 outliers final: 45 residues processed: 362 average time/residue: 0.6829 time to fit residues: 278.5168 Evaluate side-chains 329 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 268 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 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 419 MET Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 18 LYS 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 313 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 363 SER 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 384 MET 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 26 GLU 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 243 ASP Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 317 LYS Chi-restraints excluded: chain E residue 326 GLU 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 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 321 ILE Chi-restraints excluded: chain F residue 429 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 2 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 175 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN C 302 ASN D 100 GLN D 140 GLN D 200 ASN E 167 ASN E 200 ASN F 140 GLN F 295 ASN F 359 GLN F 399 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.168398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.136963 restraints weight = 22365.738| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.26 r_work: 0.3345 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 21368 Z= 0.266 Angle : 0.684 11.451 28966 Z= 0.358 Chirality : 0.047 0.190 3246 Planarity : 0.004 0.045 3599 Dihedral : 11.480 173.376 2996 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 5.27 % Allowed : 14.70 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.16), residues: 2580 helix: 1.03 (0.14), residues: 1362 sheet: -0.02 (0.29), residues: 335 loop : -1.41 (0.19), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 177 TYR 0.022 0.002 TYR B 312 PHE 0.027 0.003 PHE D 65 TRP 0.016 0.002 TRP B 162 HIS 0.006 0.002 HIS E 8 Details of bonding type rmsd covalent geometry : bond 0.00631 (21368) covalent geometry : angle 0.68394 (28966) hydrogen bonds : bond 0.04473 ( 1056) hydrogen bonds : angle 5.06230 ( 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 411 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 293 time to evaluate : 0.943 Fit side-chains REVERT: A 79 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7993 (mtpm) REVERT: A 140 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7693 (mt0) REVERT: A 333 LYS cc_start: 0.7195 (OUTLIER) cc_final: 0.6914 (mmmt) REVERT: A 337 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7185 (mp0) REVERT: A 355 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8066 (mm-40) REVERT: A 370 ASP cc_start: 0.6245 (m-30) cc_final: 0.5551 (t70) REVERT: A 411 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7308 (ttmm) REVERT: A 414 TRP cc_start: 0.7606 (m100) cc_final: 0.7138 (m-90) REVERT: A 427 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7920 (ttpp) REVERT: B 96 LYS cc_start: 0.8640 (mtpp) cc_final: 0.8355 (mttm) REVERT: B 109 LYS cc_start: 0.8587 (ttmm) cc_final: 0.8346 (tttt) REVERT: B 274 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7351 (mtm-85) REVERT: B 405 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7740 (tttp) REVERT: C 13 GLN cc_start: 0.7406 (tp40) cc_final: 0.7194 (tp40) REVERT: C 18 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.7109 (tmtp) REVERT: C 41 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7299 (tttt) REVERT: C 92 LYS cc_start: 0.8377 (mmmm) cc_final: 0.8019 (mppt) REVERT: C 128 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6546 (mtt) REVERT: D 3 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7630 (mp0) REVERT: D 26 GLU cc_start: 0.7848 (mp0) cc_final: 0.7622 (mp0) REVERT: D 136 ASP cc_start: 0.7563 (t70) cc_final: 0.7280 (t0) REVERT: D 153 ASP cc_start: 0.7933 (t0) cc_final: 0.7394 (t70) REVERT: D 157 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7198 (m-30) REVERT: D 331 THR cc_start: 0.7774 (p) cc_final: 0.7510 (m) REVERT: D 389 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7988 (tp30) REVERT: D 429 VAL cc_start: 0.8980 (OUTLIER) cc_final: 0.8600 (t) REVERT: E 26 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7832 (mt-10) REVERT: E 92 LYS cc_start: 0.8669 (tppp) cc_final: 0.8229 (ttmt) REVERT: E 109 LYS cc_start: 0.8416 (tptt) cc_final: 0.7805 (tttp) REVERT: E 170 ARG cc_start: 0.7015 (ptt-90) cc_final: 0.6017 (mtp85) REVERT: E 196 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7726 (ppp) REVERT: E 279 GLN cc_start: 0.7047 (pt0) cc_final: 0.6078 (tp40) REVERT: E 317 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6478 (ptmt) REVERT: E 326 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6788 (mt-10) REVERT: E 371 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7817 (pt) REVERT: E 413 LYS cc_start: 0.8262 (ttmt) cc_final: 0.7891 (mttt) REVERT: F 147 ASP cc_start: 0.7935 (m-30) cc_final: 0.7392 (p0) REVERT: F 243 ASP cc_start: 0.7692 (m-30) cc_final: 0.7167 (t0) REVERT: F 327 ASN cc_start: 0.6991 (p0) cc_final: 0.6527 (p0) REVERT: F 333 LYS cc_start: 0.7637 (ttpp) cc_final: 0.7201 (ttmt) REVERT: F 347 GLU cc_start: 0.7447 (mp0) cc_final: 0.6979 (mm-30) REVERT: F 397 GLU cc_start: 0.6986 (tp30) cc_final: 0.6039 (tm-30) REVERT: F 398 GLN cc_start: 0.7649 (mt0) cc_final: 0.7001 (mp10) REVERT: F 407 ARG cc_start: 0.7344 (ttp-170) cc_final: 0.6483 (ttm170) REVERT: F 413 LYS cc_start: 0.6522 (OUTLIER) cc_final: 0.6088 (mtmp) REVERT: F 431 ILE cc_start: 0.7210 (OUTLIER) cc_final: 0.6775 (pt) outliers start: 118 outliers final: 52 residues processed: 371 average time/residue: 0.6800 time to fit residues: 284.3780 Evaluate side-chains 338 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 265 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 355 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 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 274 ARG Chi-restraints excluded: chain B residue 292 SER 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 B residue 405 LYS Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 41 LYS 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 319 CYS Chi-restraints excluded: chain C residue 326 GLU 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 157 ASP 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 384 MET 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 26 GLU 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 244 VAL 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 326 GLU 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 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 413 LYS 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: 7.9990 chunk 166 optimal weight: 5.9990 chunk 175 optimal weight: 6.9990 chunk 226 optimal weight: 0.7980 chunk 177 optimal weight: 8.9990 chunk 227 optimal weight: 0.7980 chunk 174 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 179 optimal weight: 20.0000 chunk 123 optimal weight: 0.9980 chunk 65 optimal weight: 0.0980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 ASN C 288 ASN C 302 ASN D 62 ASN D 100 GLN D 140 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.172118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.141135 restraints weight = 22478.487| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.15 r_work: 0.3409 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2997 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= 0.127 Angle : 0.552 9.583 28966 Z= 0.294 Chirality : 0.041 0.228 3246 Planarity : 0.003 0.034 3599 Dihedral : 11.225 173.115 2996 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.62 % Allowed : 17.16 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.17), residues: 2580 helix: 1.41 (0.15), residues: 1361 sheet: 0.01 (0.29), residues: 330 loop : -1.34 (0.19), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 236 TYR 0.013 0.001 TYR F 149 PHE 0.015 0.001 PHE D 65 TRP 0.013 0.001 TRP F 154 HIS 0.006 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00279 (21368) covalent geometry : angle 0.55163 (28966) hydrogen bonds : bond 0.03512 ( 1056) hydrogen bonds : angle 4.77318 ( 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 375 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 294 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7891 (mtpm) REVERT: A 136 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.6757 (t0) REVERT: A 140 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7513 (mt0) REVERT: A 315 ILE cc_start: 0.6699 (OUTLIER) cc_final: 0.6289 (mp) REVERT: A 333 LYS cc_start: 0.7208 (OUTLIER) cc_final: 0.6898 (mmmm) REVERT: A 337 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7076 (mp0) REVERT: A 370 ASP cc_start: 0.6268 (m-30) cc_final: 0.5571 (t70) REVERT: A 414 TRP cc_start: 0.7558 (m100) cc_final: 0.7180 (m-90) REVERT: A 427 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7889 (ttpp) REVERT: B 96 LYS cc_start: 0.8576 (mtpp) cc_final: 0.8241 (mttt) REVERT: B 274 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7326 (mtm-85) REVERT: C 18 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.7164 (tmtp) REVERT: C 92 LYS cc_start: 0.8366 (mmmm) cc_final: 0.8021 (mppt) REVERT: C 128 MET cc_start: 0.6986 (OUTLIER) cc_final: 0.6499 (mtt) REVERT: D 1 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8176 (ptp) REVERT: D 136 ASP cc_start: 0.7511 (t70) cc_final: 0.7180 (t0) REVERT: D 153 ASP cc_start: 0.7886 (t0) cc_final: 0.7324 (t70) REVERT: D 331 THR cc_start: 0.7647 (p) cc_final: 0.7376 (m) REVERT: E 92 LYS cc_start: 0.8620 (tppp) cc_final: 0.8308 (ttpt) REVERT: E 109 LYS cc_start: 0.8349 (tptt) cc_final: 0.7824 (tttp) REVERT: E 124 ARG cc_start: 0.6510 (OUTLIER) cc_final: 0.6161 (mtm180) REVERT: E 170 ARG cc_start: 0.7006 (ptt-90) cc_final: 0.6056 (mtp85) REVERT: E 243 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7211 (m-30) REVERT: E 413 LYS cc_start: 0.8176 (ttmt) cc_final: 0.7865 (mttt) REVERT: F 147 ASP cc_start: 0.7908 (m-30) cc_final: 0.7380 (p0) REVERT: F 243 ASP cc_start: 0.7611 (m-30) cc_final: 0.7065 (t0) REVERT: F 302 ASN cc_start: 0.7714 (t0) cc_final: 0.7296 (t0) REVERT: F 327 ASN cc_start: 0.6916 (p0) cc_final: 0.6465 (p0) REVERT: F 333 LYS cc_start: 0.7653 (ttpp) cc_final: 0.7215 (ttmt) REVERT: F 347 GLU cc_start: 0.7486 (mp0) cc_final: 0.6997 (mm-30) REVERT: F 384 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7780 (ttp) REVERT: F 397 GLU cc_start: 0.7025 (tp30) cc_final: 0.6001 (tm-30) REVERT: F 398 GLN cc_start: 0.7637 (mt0) cc_final: 0.6951 (mp-120) REVERT: F 407 ARG cc_start: 0.7322 (ttp-170) cc_final: 0.6614 (ttm170) REVERT: F 431 ILE cc_start: 0.7206 (OUTLIER) cc_final: 0.6804 (pt) outliers start: 81 outliers final: 37 residues processed: 349 average time/residue: 0.6957 time to fit residues: 274.0309 Evaluate side-chains 316 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 265 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 136 ASP Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 315 ILE 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 131 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 18 LYS 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 243 ASP Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain 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 118 GLU Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 244 VAL 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 E residue 380 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 384 MET Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 431 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 221 optimal weight: 0.4980 chunk 85 optimal weight: 0.9980 chunk 99 optimal weight: 0.0570 chunk 62 optimal weight: 0.7980 chunk 6 optimal weight: 0.0000 chunk 133 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 243 optimal weight: 6.9990 chunk 253 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 overall best weight: 0.4702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 167 ASN C 288 ASN C 302 ASN D 62 ASN D 100 GLN 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 F 359 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.175431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.144839 restraints weight = 22552.825| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.10 r_work: 0.3464 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21368 Z= 0.107 Angle : 0.527 10.191 28966 Z= 0.278 Chirality : 0.040 0.231 3246 Planarity : 0.003 0.051 3599 Dihedral : 10.970 174.248 2996 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.17 % Allowed : 18.28 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.17), residues: 2580 helix: 1.71 (0.15), residues: 1356 sheet: 0.07 (0.30), residues: 334 loop : -1.33 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 236 TYR 0.015 0.001 TYR A 312 PHE 0.012 0.001 PHE D 65 TRP 0.013 0.001 TRP A 89 HIS 0.005 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00229 (21368) covalent geometry : angle 0.52688 (28966) hydrogen bonds : bond 0.03117 ( 1056) hydrogen bonds : angle 4.55800 ( 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 358 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 287 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7893 (mtpm) REVERT: A 140 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7617 (mt0) REVERT: A 315 ILE cc_start: 0.6632 (OUTLIER) cc_final: 0.6278 (mp) REVERT: A 333 LYS cc_start: 0.7166 (ttpt) cc_final: 0.6902 (mmmm) REVERT: A 337 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7023 (mp0) REVERT: A 370 ASP cc_start: 0.6296 (m-30) cc_final: 0.5672 (t70) REVERT: A 414 TRP cc_start: 0.7530 (m100) cc_final: 0.7187 (m-90) REVERT: A 419 MET cc_start: 0.7742 (tpp) cc_final: 0.7377 (mmt) REVERT: A 427 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7858 (ttpp) REVERT: B 96 LYS cc_start: 0.8543 (mtpp) cc_final: 0.8216 (mttt) REVERT: C 92 LYS cc_start: 0.8363 (mmmm) cc_final: 0.8049 (mppt) REVERT: C 391 GLU cc_start: 0.7757 (mp0) cc_final: 0.7348 (mp0) REVERT: D 1 MET cc_start: 0.8504 (ptp) cc_final: 0.8166 (ptm) REVERT: D 136 ASP cc_start: 0.7478 (t70) cc_final: 0.7226 (t0) REVERT: D 153 ASP cc_start: 0.7820 (t0) cc_final: 0.7237 (t70) REVERT: D 331 THR cc_start: 0.7640 (p) cc_final: 0.7345 (m) REVERT: E 92 LYS cc_start: 0.8517 (tppp) cc_final: 0.8137 (ttmt) REVERT: E 109 LYS cc_start: 0.8259 (tptt) cc_final: 0.7792 (tttt) REVERT: E 170 ARG cc_start: 0.7000 (ptt-90) cc_final: 0.6114 (mtp85) REVERT: E 243 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7063 (m-30) REVERT: E 392 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7305 (pp20) REVERT: E 413 LYS cc_start: 0.8067 (ttmt) cc_final: 0.7865 (mttt) REVERT: F 147 ASP cc_start: 0.7859 (m-30) cc_final: 0.7386 (p0) REVERT: F 243 ASP cc_start: 0.7456 (m-30) cc_final: 0.6932 (t0) REVERT: F 296 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6861 (tm-30) REVERT: F 327 ASN cc_start: 0.6861 (p0) cc_final: 0.6398 (p0) REVERT: F 333 LYS cc_start: 0.7678 (ttpp) cc_final: 0.7200 (ttmt) REVERT: F 347 GLU cc_start: 0.7460 (mp0) cc_final: 0.6974 (mm-30) REVERT: F 384 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7711 (ttp) REVERT: F 397 GLU cc_start: 0.7016 (tp30) cc_final: 0.6009 (tm-30) REVERT: F 398 GLN cc_start: 0.7652 (mt0) cc_final: 0.7015 (mp-120) REVERT: F 407 ARG cc_start: 0.7309 (ttp-170) cc_final: 0.6692 (ttm170) REVERT: F 431 ILE cc_start: 0.7146 (OUTLIER) cc_final: 0.6808 (pt) outliers start: 71 outliers final: 25 residues processed: 331 average time/residue: 0.6877 time to fit residues: 257.3504 Evaluate side-chains 296 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 263 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 315 ILE 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 330 THR Chi-restraints excluded: chain B residue 356 VAL 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 304 VAL Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 251 ASP 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 296 GLU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 384 MET Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 431 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 142 optimal weight: 8.9990 chunk 209 optimal weight: 5.9990 chunk 238 optimal weight: 6.9990 chunk 253 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 255 optimal weight: 0.0370 chunk 180 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 191 optimal weight: 0.9990 overall best weight: 1.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN C 167 ASN C 288 ASN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.172608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.142496 restraints weight = 22527.726| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.11 r_work: 0.3405 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21368 Z= 0.147 Angle : 0.565 11.431 28966 Z= 0.295 Chirality : 0.042 0.250 3246 Planarity : 0.004 0.042 3599 Dihedral : 11.032 172.781 2996 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.26 % Allowed : 18.50 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.17), residues: 2580 helix: 1.67 (0.15), residues: 1355 sheet: 0.03 (0.29), residues: 336 loop : -1.32 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 139 TYR 0.021 0.001 TYR A 312 PHE 0.018 0.002 PHE D 65 TRP 0.012 0.001 TRP B 162 HIS 0.007 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00341 (21368) covalent geometry : angle 0.56493 (28966) hydrogen bonds : bond 0.03421 ( 1056) hydrogen bonds : angle 4.60749 ( 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 350 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 277 time to evaluate : 0.864 Fit side-chains REVERT: A 79 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7967 (mtpm) REVERT: A 136 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.6922 (t0) REVERT: A 140 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7577 (mt0) REVERT: A 246 LEU cc_start: 0.7690 (tp) cc_final: 0.7484 (mt) REVERT: A 315 ILE cc_start: 0.6653 (OUTLIER) cc_final: 0.6270 (mp) REVERT: A 333 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6933 (mmmm) REVERT: A 337 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7102 (mp0) REVERT: A 370 ASP cc_start: 0.6331 (m-30) cc_final: 0.5685 (t70) REVERT: A 414 TRP cc_start: 0.7599 (m100) cc_final: 0.7226 (m-90) REVERT: A 427 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7901 (ttpp) REVERT: B 96 LYS cc_start: 0.8596 (mtpp) cc_final: 0.8264 (mttt) REVERT: B 231 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8051 (mp0) REVERT: C 92 LYS cc_start: 0.8390 (mmmm) cc_final: 0.8078 (mppt) REVERT: C 391 GLU cc_start: 0.7793 (mp0) cc_final: 0.7376 (mp0) REVERT: D 1 MET cc_start: 0.8599 (ptp) cc_final: 0.8245 (ptm) REVERT: D 136 ASP cc_start: 0.7564 (t70) cc_final: 0.7280 (t0) REVERT: D 153 ASP cc_start: 0.7912 (t0) cc_final: 0.7322 (t70) REVERT: D 331 THR cc_start: 0.7701 (p) cc_final: 0.7412 (m) REVERT: E 92 LYS cc_start: 0.8610 (tppp) cc_final: 0.8215 (ttmt) REVERT: E 109 LYS cc_start: 0.8345 (tptt) cc_final: 0.7911 (tptt) REVERT: E 170 ARG cc_start: 0.7050 (ptt-90) cc_final: 0.6104 (mtp180) REVERT: E 196 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7608 (ppp) REVERT: E 243 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7110 (m-30) REVERT: E 389 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7275 (tt0) REVERT: E 392 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7350 (pp20) REVERT: E 413 LYS cc_start: 0.8044 (ttmt) cc_final: 0.7826 (mttt) REVERT: F 147 ASP cc_start: 0.7950 (m-30) cc_final: 0.7444 (p0) REVERT: F 243 ASP cc_start: 0.7379 (m-30) cc_final: 0.6843 (t0) REVERT: F 296 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6819 (tm-30) REVERT: F 327 ASN cc_start: 0.6937 (p0) cc_final: 0.6475 (p0) REVERT: F 333 LYS cc_start: 0.7681 (ttpp) cc_final: 0.7252 (ttmt) REVERT: F 347 GLU cc_start: 0.7485 (mp0) cc_final: 0.6985 (mm-30) REVERT: F 359 GLN cc_start: 0.7011 (pm20) cc_final: 0.6750 (pm20) REVERT: F 384 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7858 (ttp) REVERT: F 397 GLU cc_start: 0.7059 (tp30) cc_final: 0.6031 (tm-30) REVERT: F 398 GLN cc_start: 0.7695 (mt0) cc_final: 0.7065 (mp-120) REVERT: F 407 ARG cc_start: 0.7354 (ttp-170) cc_final: 0.6714 (ttm170) REVERT: F 431 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.6828 (pt) outliers start: 73 outliers final: 40 residues processed: 323 average time/residue: 0.6994 time to fit residues: 254.8709 Evaluate side-chains 322 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 269 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 167 ASN Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 71 SER 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 384 MET 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 100 GLN Chi-restraints excluded: chain E residue 118 GLU 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 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 F residue 19 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 296 GLU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 384 MET Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 431 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 0.3980 chunk 194 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 217 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 92 optimal weight: 0.4980 chunk 131 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 253 HIS C 167 ASN C 302 ASN D 100 GLN D 200 ASN E 140 GLN E 167 ASN E 200 ASN F 140 GLN F 295 ASN F 399 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.173907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.144511 restraints weight = 22482.798| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.10 r_work: 0.3416 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21368 Z= 0.123 Angle : 0.550 12.503 28966 Z= 0.287 Chirality : 0.041 0.200 3246 Planarity : 0.003 0.037 3599 Dihedral : 10.987 174.215 2996 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.17 % Allowed : 18.95 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.17), residues: 2580 helix: 1.75 (0.15), residues: 1348 sheet: 0.03 (0.29), residues: 332 loop : -1.35 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 139 TYR 0.022 0.001 TYR A 312 PHE 0.015 0.001 PHE D 65 TRP 0.012 0.001 TRP B 162 HIS 0.007 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00277 (21368) covalent geometry : angle 0.55025 (28966) hydrogen bonds : bond 0.03254 ( 1056) hydrogen bonds : angle 4.56116 ( 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 345 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 274 time to evaluate : 0.868 Fit side-chains REVERT: A 79 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7884 (mtpm) REVERT: A 140 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7501 (mt0) REVERT: A 315 ILE cc_start: 0.6498 (OUTLIER) cc_final: 0.6138 (mp) REVERT: A 333 LYS cc_start: 0.7113 (OUTLIER) cc_final: 0.6843 (mmmm) REVERT: A 337 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6890 (mp0) REVERT: A 368 MET cc_start: 0.6397 (ttp) cc_final: 0.6097 (ttp) REVERT: A 369 SER cc_start: 0.6271 (OUTLIER) cc_final: 0.5962 (t) REVERT: A 370 ASP cc_start: 0.6329 (m-30) cc_final: 0.5645 (t70) REVERT: A 414 TRP cc_start: 0.7427 (m100) cc_final: 0.7191 (m-90) REVERT: A 427 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7757 (ttpp) REVERT: B 96 LYS cc_start: 0.8428 (mtpp) cc_final: 0.8126 (mttt) REVERT: C 92 LYS cc_start: 0.8187 (mmmm) cc_final: 0.7927 (mppt) REVERT: C 391 GLU cc_start: 0.7681 (mp0) cc_final: 0.7289 (mp0) REVERT: D 1 MET cc_start: 0.8409 (ptp) cc_final: 0.8056 (ptm) REVERT: D 136 ASP cc_start: 0.7367 (t70) cc_final: 0.7073 (t70) REVERT: D 139 ARG cc_start: 0.7683 (ttp80) cc_final: 0.7478 (ttp80) REVERT: D 153 ASP cc_start: 0.7751 (t0) cc_final: 0.7183 (t70) REVERT: D 300 LYS cc_start: 0.7304 (mttt) cc_final: 0.6915 (mtpt) REVERT: D 331 THR cc_start: 0.7612 (p) cc_final: 0.7321 (m) REVERT: E 92 LYS cc_start: 0.8460 (tppp) cc_final: 0.8083 (ttmt) REVERT: E 109 LYS cc_start: 0.8199 (tptt) cc_final: 0.7786 (tptt) REVERT: E 170 ARG cc_start: 0.6906 (ptt-90) cc_final: 0.6084 (mtp85) REVERT: E 243 ASP cc_start: 0.7216 (OUTLIER) cc_final: 0.6860 (m-30) REVERT: E 392 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7368 (pp20) REVERT: F 147 ASP cc_start: 0.7660 (m-30) cc_final: 0.7347 (p0) REVERT: F 243 ASP cc_start: 0.7189 (m-30) cc_final: 0.6781 (t0) REVERT: F 251 ASP cc_start: 0.6563 (m-30) cc_final: 0.6267 (p0) REVERT: F 296 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6749 (tm-30) REVERT: F 327 ASN cc_start: 0.6869 (p0) cc_final: 0.6403 (p0) REVERT: F 333 LYS cc_start: 0.7545 (ttpp) cc_final: 0.7075 (ttmt) REVERT: F 347 GLU cc_start: 0.7371 (mp0) cc_final: 0.6983 (mm-30) REVERT: F 359 GLN cc_start: 0.6935 (pm20) cc_final: 0.6670 (pm20) REVERT: F 384 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7625 (ttp) REVERT: F 397 GLU cc_start: 0.6948 (tp30) cc_final: 0.6036 (tm-30) REVERT: F 398 GLN cc_start: 0.7611 (mt0) cc_final: 0.7069 (mp-120) REVERT: F 431 ILE cc_start: 0.7177 (OUTLIER) cc_final: 0.6808 (pt) outliers start: 71 outliers final: 44 residues processed: 323 average time/residue: 0.6807 time to fit residues: 249.3307 Evaluate side-chains 314 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 260 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 315 ILE Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 265 LYS 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 137 ILE Chi-restraints excluded: chain C residue 167 ASN Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 71 SER 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 384 MET 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 100 GLN Chi-restraints excluded: chain E residue 118 GLU 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 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 19 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 296 GLU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 384 MET Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 431 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 180 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 HIS C 167 ASN C 302 ASN D 100 GLN D 200 ASN E 140 GLN E 167 ASN E 200 ASN F 140 GLN F 295 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.173679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.143215 restraints weight = 22674.409| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.17 r_work: 0.3430 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21368 Z= 0.129 Angle : 0.559 11.506 28966 Z= 0.292 Chirality : 0.041 0.208 3246 Planarity : 0.003 0.035 3599 Dihedral : 10.972 174.243 2996 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.86 % Allowed : 19.30 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.17), residues: 2580 helix: 1.73 (0.15), residues: 1348 sheet: 0.01 (0.29), residues: 332 loop : -1.34 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 139 TYR 0.018 0.001 TYR C 312 PHE 0.014 0.001 PHE D 65 TRP 0.012 0.001 TRP B 162 HIS 0.008 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00295 (21368) covalent geometry : angle 0.55897 (28966) hydrogen bonds : bond 0.03273 ( 1056) hydrogen bonds : angle 4.56339 ( 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 337 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 273 time to evaluate : 0.831 Fit side-chains REVERT: A 79 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7930 (mtpm) REVERT: A 140 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7690 (mt0) REVERT: A 333 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6905 (mmmm) REVERT: A 337 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7105 (mp0) REVERT: A 368 MET cc_start: 0.6319 (ttp) cc_final: 0.6029 (ttp) REVERT: A 369 SER cc_start: 0.5841 (OUTLIER) cc_final: 0.5533 (t) REVERT: A 370 ASP cc_start: 0.6235 (m-30) cc_final: 0.5554 (t70) REVERT: A 414 TRP cc_start: 0.7592 (m100) cc_final: 0.7210 (m-90) REVERT: A 427 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7854 (ttpp) REVERT: B 96 LYS cc_start: 0.8566 (mtpp) cc_final: 0.8240 (mttt) REVERT: C 13 GLN cc_start: 0.7508 (tp40) cc_final: 0.7300 (tp40) REVERT: C 92 LYS cc_start: 0.8366 (mmmm) cc_final: 0.8063 (mppt) REVERT: C 391 GLU cc_start: 0.7783 (mp0) cc_final: 0.7378 (mp0) REVERT: D 1 MET cc_start: 0.8549 (ptp) cc_final: 0.8161 (ptm) REVERT: D 136 ASP cc_start: 0.7549 (t70) cc_final: 0.7241 (t0) REVERT: D 139 ARG cc_start: 0.7829 (ttp80) cc_final: 0.7626 (ttp80) REVERT: D 153 ASP cc_start: 0.7866 (t0) cc_final: 0.7529 (t0) REVERT: D 300 LYS cc_start: 0.7266 (mttt) cc_final: 0.6937 (mtpt) REVERT: D 331 THR cc_start: 0.7671 (p) cc_final: 0.7376 (m) REVERT: E 92 LYS cc_start: 0.8547 (tppp) cc_final: 0.8158 (ttmt) REVERT: E 100 GLN cc_start: 0.7943 (pt0) cc_final: 0.7634 (mp10) REVERT: E 109 LYS cc_start: 0.8306 (tptt) cc_final: 0.7897 (tptt) REVERT: E 170 ARG cc_start: 0.7030 (ptt-90) cc_final: 0.6087 (mtp180) REVERT: E 196 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7516 (ppp) REVERT: E 243 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.7082 (m-30) REVERT: E 345 GLU cc_start: 0.6880 (tm-30) cc_final: 0.6331 (tt0) REVERT: E 392 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7341 (pp20) REVERT: F 147 ASP cc_start: 0.7942 (m-30) cc_final: 0.7433 (p0) REVERT: F 243 ASP cc_start: 0.7359 (m-30) cc_final: 0.6848 (t0) REVERT: F 251 ASP cc_start: 0.6669 (m-30) cc_final: 0.6253 (p0) REVERT: F 296 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6762 (tm-30) REVERT: F 302 ASN cc_start: 0.7553 (t0) cc_final: 0.7121 (t0) REVERT: F 327 ASN cc_start: 0.6832 (p0) cc_final: 0.6386 (p0) REVERT: F 333 LYS cc_start: 0.7543 (ttpp) cc_final: 0.7197 (ttmt) REVERT: F 347 GLU cc_start: 0.7424 (mp0) cc_final: 0.6950 (mm-30) REVERT: F 359 GLN cc_start: 0.7037 (pm20) cc_final: 0.6731 (pm20) REVERT: F 373 GLU cc_start: 0.6243 (mt-10) cc_final: 0.5457 (mp0) REVERT: F 384 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7777 (ttp) REVERT: F 397 GLU cc_start: 0.7024 (tp30) cc_final: 0.6099 (tm-30) REVERT: F 398 GLN cc_start: 0.7298 (mt0) cc_final: 0.6748 (mp-120) REVERT: F 431 ILE cc_start: 0.7251 (OUTLIER) cc_final: 0.6865 (pt) outliers start: 64 outliers final: 42 residues processed: 318 average time/residue: 0.6842 time to fit residues: 246.0226 Evaluate side-chains 317 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 265 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 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 265 LYS 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 137 ILE Chi-restraints excluded: chain C residue 167 ASN Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 118 GLU 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 365 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 296 GLU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 384 MET Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 431 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 29 optimal weight: 4.9990 chunk 214 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 238 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 216 optimal weight: 10.0000 chunk 37 optimal weight: 0.3980 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 167 ASN C 288 ASN C 302 ASN D 200 ASN E 140 GLN E 167 ASN E 200 ASN F 140 GLN F 200 ASN F 295 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.168516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.138146 restraints weight = 22660.804| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.99 r_work: 0.3367 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 21368 Z= 0.251 Angle : 0.700 13.703 28966 Z= 0.361 Chirality : 0.046 0.332 3246 Planarity : 0.004 0.045 3599 Dihedral : 11.411 172.816 2996 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.40 % Allowed : 18.90 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.16), residues: 2580 helix: 1.22 (0.14), residues: 1353 sheet: -0.09 (0.29), residues: 335 loop : -1.38 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 236 TYR 0.030 0.002 TYR C 312 PHE 0.026 0.003 PHE D 65 TRP 0.021 0.002 TRP D 162 HIS 0.008 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00596 (21368) covalent geometry : angle 0.69973 (28966) hydrogen bonds : bond 0.04221 ( 1056) hydrogen bonds : angle 4.90727 ( 3033) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8961.53 seconds wall clock time: 153 minutes 36.68 seconds (9216.68 seconds total)