Starting phenix.real_space_refine on Mon Jan 20 07:00:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ord_17120/01_2025/8ord_17120.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ord_17120/01_2025/8ord_17120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ord_17120/01_2025/8ord_17120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ord_17120/01_2025/8ord_17120.map" model { file = "/net/cci-nas-00/data/ceres_data/8ord_17120/01_2025/8ord_17120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ord_17120/01_2025/8ord_17120.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.002 sd= 1.102 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: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 105 5.16 5 C 9195 2.51 5 N 2460 2.21 5 O 2815 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 138 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 14590 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2886 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "B" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2886 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "C" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2886 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "D" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2886 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "E" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2886 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'PO4': 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: {'ADP': 1, 'PO4': 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: {'ADP': 1, 'PO4': 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: {'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.39, per 1000 atoms: 0.71 Number of scatterers: 14590 At special positions: 0 Unit cell: (162.44, 96.416, 137.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 105 16.00 P 15 15.00 O 2815 8.00 N 2460 7.00 C 9195 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.61 Conformation dependent library (CDL) restraints added in 1.6 seconds 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3400 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 30 sheets defined 51.7% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 removed outlier: 3.677A pdb=" N LYS A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 94 removed outlier: 3.562A pdb=" N MET A 84 " --> pdb=" O ASN A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 103 removed outlier: 3.713A pdb=" N GLU A 102 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.955A pdb=" N ARG A 118 " --> pdb=" O PRO A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 147 Processing helix chain 'A' and resid 174 through 177 Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.668A pdb=" N THR A 196 " --> pdb=" O MET A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 204 through 219 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 254 through 259 removed outlier: 3.697A pdb=" N CYS A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 291 through 297 Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.603A pdb=" N THR A 306 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 339 through 351 removed outlier: 3.540A pdb=" N GLY A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 355 Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.650A pdb=" N GLU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.858A pdb=" N VAL A 372 " --> pdb=" O PRO A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 80 through 94 removed outlier: 3.566A pdb=" N MET B 84 " --> pdb=" O ASN B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 103 removed outlier: 3.939A pdb=" N GLU B 102 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 128 removed outlier: 4.115A pdb=" N ARG B 118 " --> pdb=" O PRO B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 147 Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 183 through 196 removed outlier: 3.655A pdb=" N THR B 196 " --> pdb=" O MET B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 199 No H-bonds generated for 'chain 'B' and resid 197 through 199' Processing helix chain 'B' and resid 204 through 219 removed outlier: 3.804A pdb=" N GLU B 209 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS B 219 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 235 removed outlier: 3.614A pdb=" N GLU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 262 removed outlier: 3.634A pdb=" N CYS B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Proline residue: B 260 - end of helix Processing helix chain 'B' and resid 263 through 264 No H-bonds generated for 'chain 'B' and resid 263 through 264' Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 275 through 286 Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 291 through 297 Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.566A pdb=" N THR B 306 " --> pdb=" O GLY B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 323 Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 339 through 349 removed outlier: 4.156A pdb=" N GLY B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B 346 " --> pdb=" O TRP B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 removed outlier: 6.233A pdb=" N THR B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 368 removed outlier: 3.788A pdb=" N GLU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 375 removed outlier: 4.146A pdb=" N ARG B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS B 375 " --> pdb=" O ILE B 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 370 through 375' Processing helix chain 'C' and resid 57 through 63 removed outlier: 3.761A pdb=" N LYS C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 94 removed outlier: 3.777A pdb=" N MET C 84 " --> pdb=" O ASN C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 103 Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.905A pdb=" N ARG C 118 " --> pdb=" O PRO C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 147 Processing helix chain 'C' and resid 174 through 177 Processing helix chain 'C' and resid 183 through 196 removed outlier: 3.945A pdb=" N THR C 196 " --> pdb=" O MET C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 199 No H-bonds generated for 'chain 'C' and resid 197 through 199' Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.530A pdb=" N ILE C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 235 Processing helix chain 'C' and resid 254 through 259 removed outlier: 3.694A pdb=" N CYS C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 265 through 269 Processing helix chain 'C' and resid 275 through 286 Processing helix chain 'C' and resid 288 through 290 No H-bonds generated for 'chain 'C' and resid 288 through 290' Processing helix chain 'C' and resid 291 through 297 Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 310 through 323 Processing helix chain 'C' and resid 336 through 338 No H-bonds generated for 'chain 'C' and resid 336 through 338' Processing helix chain 'C' and resid 339 through 350 removed outlier: 3.778A pdb=" N GLY C 345 " --> pdb=" O VAL C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 355 Processing helix chain 'C' and resid 361 through 368 removed outlier: 3.577A pdb=" N GLU C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 375 removed outlier: 3.712A pdb=" N VAL C 372 " --> pdb=" O PRO C 369 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS C 373 " --> pdb=" O SER C 370 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS C 375 " --> pdb=" O VAL C 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 63 removed outlier: 3.694A pdb=" N LYS D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 94 Processing helix chain 'D' and resid 99 through 103 Processing helix chain 'D' and resid 114 through 128 removed outlier: 3.854A pdb=" N ARG D 118 " --> pdb=" O PRO D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 147 Processing helix chain 'D' and resid 174 through 177 removed outlier: 3.635A pdb=" N ILE D 177 " --> pdb=" O PRO D 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 174 through 177' Processing helix chain 'D' and resid 183 through 196 removed outlier: 4.019A pdb=" N THR D 196 " --> pdb=" O MET D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 199 No H-bonds generated for 'chain 'D' and resid 197 through 199' Processing helix chain 'D' and resid 204 through 219 removed outlier: 3.774A pdb=" N GLU D 209 " --> pdb=" O THR D 205 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 235 Processing helix chain 'D' and resid 254 through 259 removed outlier: 3.815A pdb=" N CYS D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 265 through 270 Processing helix chain 'D' and resid 275 through 286 Processing helix chain 'D' and resid 288 through 290 No H-bonds generated for 'chain 'D' and resid 288 through 290' Processing helix chain 'D' and resid 291 through 297 Processing helix chain 'D' and resid 303 through 307 Processing helix chain 'D' and resid 310 through 323 Processing helix chain 'D' and resid 336 through 338 No H-bonds generated for 'chain 'D' and resid 336 through 338' Processing helix chain 'D' and resid 339 through 349 removed outlier: 3.659A pdb=" N GLY D 345 " --> pdb=" O VAL D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 355 removed outlier: 6.030A pdb=" N THR D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 368 removed outlier: 3.606A pdb=" N GLU D 366 " --> pdb=" O ASP D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 376 removed outlier: 3.713A pdb=" N ARG D 374 " --> pdb=" O SER D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 63 Processing helix chain 'E' and resid 80 through 94 Processing helix chain 'E' and resid 99 through 103 removed outlier: 3.629A pdb=" N GLU E 102 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 128 removed outlier: 4.093A pdb=" N ARG E 118 " --> pdb=" O PRO E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 147 Processing helix chain 'E' and resid 174 through 177 Processing helix chain 'E' and resid 183 through 196 removed outlier: 3.751A pdb=" N THR E 196 " --> pdb=" O MET E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 204 through 219 removed outlier: 3.604A pdb=" N CYS E 219 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 235 Processing helix chain 'E' and resid 254 through 262 removed outlier: 3.571A pdb=" N CYS E 259 " --> pdb=" O GLU E 255 " (cutoff:3.500A) Proline residue: E 260 - end of helix Processing helix chain 'E' and resid 263 through 264 No H-bonds generated for 'chain 'E' and resid 263 through 264' Processing helix chain 'E' and resid 265 through 269 Processing helix chain 'E' and resid 275 through 286 Processing helix chain 'E' and resid 291 through 297 Processing helix chain 'E' and resid 303 through 307 Processing helix chain 'E' and resid 310 through 323 Processing helix chain 'E' and resid 336 through 338 No H-bonds generated for 'chain 'E' and resid 336 through 338' Processing helix chain 'E' and resid 339 through 351 removed outlier: 3.884A pdb=" N GLY E 345 " --> pdb=" O VAL E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 357 removed outlier: 3.796A pdb=" N GLN E 356 " --> pdb=" O THR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 368 removed outlier: 3.650A pdb=" N GLU E 366 " --> pdb=" O ASP E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 376 removed outlier: 3.880A pdb=" N ARG E 374 " --> pdb=" O SER E 370 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 34 removed outlier: 6.735A pdb=" N LEU A 10 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N THR A 108 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N CYS A 12 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA5, first strand: chain 'A' and resid 171 through 172 removed outlier: 6.464A pdb=" N ASN A 299 " --> pdb=" O ILE A 332 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 240 through 243 Processing sheet with id=AA7, first strand: chain 'B' and resid 31 through 34 removed outlier: 6.644A pdb=" N LEU B 10 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N THR B 108 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N CYS B 12 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA9, first strand: chain 'B' and resid 73 through 74 Processing sheet with id=AB1, first strand: chain 'B' and resid 171 through 172 Processing sheet with id=AB2, first strand: chain 'B' and resid 171 through 172 removed outlier: 6.500A pdb=" N ASN B 299 " --> pdb=" O ILE B 332 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 240 through 243 Processing sheet with id=AB4, first strand: chain 'C' and resid 31 through 34 removed outlier: 6.504A pdb=" N LEU C 10 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N THR C 108 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N CYS C 12 " --> pdb=" O THR C 108 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 55 through 56 Processing sheet with id=AB6, first strand: chain 'C' and resid 73 through 74 Processing sheet with id=AB7, first strand: chain 'C' and resid 178 through 180 removed outlier: 6.313A pdb=" N ASN C 299 " --> pdb=" O ILE C 332 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 178 through 180 removed outlier: 4.174A pdb=" N GLN D 43 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 240 through 243 Processing sheet with id=AC1, first strand: chain 'D' and resid 31 through 34 removed outlier: 6.594A pdb=" N LEU D 10 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N THR D 108 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N CYS D 12 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 55 through 56 Processing sheet with id=AC3, first strand: chain 'D' and resid 73 through 74 Processing sheet with id=AC4, first strand: chain 'D' and resid 171 through 172 Processing sheet with id=AC5, first strand: chain 'D' and resid 171 through 172 removed outlier: 7.170A pdb=" N VAL D 300 " --> pdb=" O THR D 151 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE D 153 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N SER D 302 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU D 155 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN D 299 " --> pdb=" O ILE D 332 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 240 through 243 Processing sheet with id=AC7, first strand: chain 'E' and resid 31 through 34 removed outlier: 6.520A pdb=" N LEU E 10 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N THR E 108 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N CYS E 12 " --> pdb=" O THR E 108 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 55 through 56 Processing sheet with id=AC9, first strand: chain 'E' and resid 73 through 74 Processing sheet with id=AD1, first strand: chain 'E' and resid 171 through 172 Processing sheet with id=AD2, first strand: chain 'E' and resid 171 through 172 removed outlier: 6.595A pdb=" N ASN E 299 " --> pdb=" O ILE E 332 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 240 through 243 710 hydrogen bonds defined for protein. 1809 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: 5.56 Time building geometry restraints manager: 4.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4724 1.34 - 1.46: 3171 1.46 - 1.58: 6814 1.58 - 1.70: 16 1.70 - 1.83: 185 Bond restraints: 14910 Sorted by residual: bond pdb=" CA PRO A 334 " pdb=" C PRO A 334 " ideal model delta sigma weight residual 1.514 1.532 -0.018 5.50e-03 3.31e+04 1.06e+01 bond pdb=" O3 PO4 E 402 " pdb=" P PO4 E 402 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.64e+00 bond pdb=" O3 PO4 A 402 " pdb=" P PO4 A 402 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.34e+00 bond pdb=" O3 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.32e+00 bond pdb=" O3 PO4 D 402 " pdb=" P PO4 D 402 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.15e+00 ... (remaining 14905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 19937 3.23 - 6.46: 252 6.46 - 9.69: 37 9.69 - 12.93: 3 12.93 - 16.16: 1 Bond angle restraints: 20230 Sorted by residual: angle pdb=" CB MET E 46 " pdb=" CG MET E 46 " pdb=" SD MET E 46 " ideal model delta sigma weight residual 112.70 128.86 -16.16 3.00e+00 1.11e-01 2.90e+01 angle pdb=" CA PRO C 104 " pdb=" N PRO C 104 " pdb=" CD PRO C 104 " ideal model delta sigma weight residual 112.00 105.59 6.41 1.40e+00 5.10e-01 2.09e+01 angle pdb=" CB MET D 285 " pdb=" CG MET D 285 " pdb=" SD MET D 285 " ideal model delta sigma weight residual 112.70 125.54 -12.84 3.00e+00 1.11e-01 1.83e+01 angle pdb=" CA MET E 46 " pdb=" CB MET E 46 " pdb=" CG MET E 46 " ideal model delta sigma weight residual 114.10 122.14 -8.04 2.00e+00 2.50e-01 1.62e+01 angle pdb=" CB MET B 357 " pdb=" CG MET B 357 " pdb=" SD MET B 357 " ideal model delta sigma weight residual 112.70 124.46 -11.76 3.00e+00 1.11e-01 1.54e+01 ... (remaining 20225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 8656 35.40 - 70.79: 265 70.79 - 106.19: 17 106.19 - 141.58: 4 141.58 - 176.98: 3 Dihedral angle restraints: 8945 sinusoidal: 3620 harmonic: 5325 Sorted by residual: dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual 300.00 123.02 176.98 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 115.97 -175.97 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 108.92 -168.92 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 8942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1270 0.036 - 0.072: 630 0.072 - 0.108: 257 0.108 - 0.144: 65 0.144 - 0.181: 8 Chirality restraints: 2230 Sorted by residual: chirality pdb=" CA GLN E 355 " pdb=" N GLN E 355 " pdb=" C GLN E 355 " pdb=" CB GLN E 355 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.15e-01 chirality pdb=" CG LEU E 244 " pdb=" CB LEU E 244 " pdb=" CD1 LEU E 244 " pdb=" CD2 LEU E 244 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CB ILE D 194 " pdb=" CA ILE D 194 " pdb=" CG1 ILE D 194 " pdb=" CG2 ILE D 194 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.75e-01 ... (remaining 2227 not shown) Planarity restraints: 2590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 342 " 0.037 2.00e-02 2.50e+03 3.00e-02 2.25e+01 pdb=" CG TRP B 342 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP B 342 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP B 342 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 342 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 342 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 342 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 342 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 342 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP B 342 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 88 " 0.031 2.00e-02 2.50e+03 2.85e-02 2.03e+01 pdb=" CG TRP B 88 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TRP B 88 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP B 88 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 88 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 88 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 88 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 88 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 88 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP B 88 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 342 " 0.028 2.00e-02 2.50e+03 2.73e-02 1.86e+01 pdb=" CG TRP C 342 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP C 342 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP C 342 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 342 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 342 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP C 342 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 342 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 342 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP C 342 " -0.001 2.00e-02 2.50e+03 ... (remaining 2587 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 343 2.67 - 3.23: 14784 3.23 - 3.78: 23950 3.78 - 4.34: 31965 4.34 - 4.90: 51131 Nonbonded interactions: 122173 Sorted by model distance: nonbonded pdb=" OG1 THR B 151 " pdb=" OE1 GLU B 169 " model vdw 2.109 3.040 nonbonded pdb=" OE2 GLU A 272 " pdb=" OG1 THR D 68 " model vdw 2.109 3.040 nonbonded pdb=" O GLY A 158 " pdb=" OG1 THR A 305 " model vdw 2.122 3.040 nonbonded pdb=" O GLY D 158 " pdb=" OG1 THR D 305 " model vdw 2.128 3.040 nonbonded pdb=" OH TYR E 220 " pdb=" OE2 GLU E 228 " model vdw 2.132 3.040 ... (remaining 122168 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 12.900 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: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 36.150 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 14910 Z= 0.302 Angle : 0.921 16.158 20230 Z= 0.468 Chirality : 0.050 0.181 2230 Planarity : 0.006 0.097 2590 Dihedral : 17.818 176.981 5545 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.58 % Allowed : 32.22 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.19), residues: 1840 helix: -0.60 (0.18), residues: 740 sheet: 0.30 (0.29), residues: 345 loop : 0.06 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.006 TRP B 342 HIS 0.011 0.001 HIS A 90 PHE 0.045 0.002 PHE A 354 TYR 0.054 0.002 TYR B 168 ARG 0.009 0.001 ARG C 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 569 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TRP cc_start: 0.9314 (m-90) cc_final: 0.8767 (m-90) REVERT: B 115 LYS cc_start: 0.8744 (mmtp) cc_final: 0.8210 (mmtp) REVERT: B 118 ARG cc_start: 0.7368 (ptt180) cc_final: 0.6894 (ptm-80) REVERT: B 208 ARG cc_start: 0.8543 (ttp80) cc_final: 0.8150 (ttm-80) REVERT: B 256 ARG cc_start: 0.8555 (mtm180) cc_final: 0.8255 (ttp-170) REVERT: B 272 GLU cc_start: 0.7294 (tt0) cc_final: 0.6992 (tt0) REVERT: B 351 LEU cc_start: 0.8969 (tp) cc_final: 0.8627 (tt) REVERT: C 71 TYR cc_start: 0.8582 (m-80) cc_final: 0.7735 (m-10) REVERT: C 197 GLU cc_start: 0.8198 (tt0) cc_final: 0.7735 (tt0) REVERT: D 134 MET cc_start: 0.8864 (tmm) cc_final: 0.8646 (tmm) REVERT: D 354 PHE cc_start: 0.8262 (t80) cc_final: 0.7850 (t80) REVERT: E 74 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7908 (mt-10) REVERT: E 193 LYS cc_start: 0.8968 (ttmt) cc_final: 0.8699 (ttmm) outliers start: 9 outliers final: 6 residues processed: 569 average time/residue: 0.2497 time to fit residues: 211.3531 Evaluate side-chains 509 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 503 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 243 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN B 90 HIS B 139 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.113953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.097916 restraints weight = 30996.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.101246 restraints weight = 15599.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.103504 restraints weight = 9464.349| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14910 Z= 0.239 Angle : 0.732 9.166 20230 Z= 0.356 Chirality : 0.047 0.169 2230 Planarity : 0.005 0.069 2590 Dihedral : 10.465 171.497 2090 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.37 % Allowed : 26.05 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.20), residues: 1840 helix: -0.20 (0.19), residues: 745 sheet: 0.27 (0.28), residues: 350 loop : 0.18 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 342 HIS 0.006 0.001 HIS A 277 PHE 0.014 0.001 PHE A 225 TYR 0.018 0.002 TYR B 168 ARG 0.007 0.001 ARG B 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 545 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.7750 (tp-100) cc_final: 0.7234 (tp-100) REVERT: A 103 HIS cc_start: 0.8406 (m90) cc_final: 0.8064 (m90) REVERT: A 142 LEU cc_start: 0.9277 (mt) cc_final: 0.8844 (mt) REVERT: A 145 TYR cc_start: 0.8139 (m-80) cc_final: 0.7276 (m-10) REVERT: A 212 ARG cc_start: 0.8454 (ttp80) cc_final: 0.8247 (tmm-80) REVERT: A 354 PHE cc_start: 0.8631 (t80) cc_final: 0.8259 (t80) REVERT: B 80 ASN cc_start: 0.8738 (t0) cc_final: 0.8477 (t0) REVERT: B 84 MET cc_start: 0.8399 (tpp) cc_final: 0.7136 (tpp) REVERT: B 88 TRP cc_start: 0.9381 (m-90) cc_final: 0.8772 (m-90) REVERT: B 115 LYS cc_start: 0.8915 (mmtp) cc_final: 0.8693 (mmmt) REVERT: B 123 GLN cc_start: 0.9152 (tt0) cc_final: 0.8399 (tp40) REVERT: B 134 MET cc_start: 0.8795 (ppp) cc_final: 0.8530 (tmm) REVERT: B 179 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.6650 (ttm170) REVERT: B 208 ARG cc_start: 0.8454 (ttp80) cc_final: 0.8149 (ttm-80) REVERT: B 272 GLU cc_start: 0.7515 (tt0) cc_final: 0.7278 (tt0) REVERT: B 316 GLN cc_start: 0.9104 (tm-30) cc_final: 0.8854 (tm-30) REVERT: C 248 GLN cc_start: 0.8783 (tt0) cc_final: 0.8064 (mt0) REVERT: C 286 LYS cc_start: 0.8915 (ttmm) cc_final: 0.8619 (mtpp) REVERT: C 327 MET cc_start: 0.8259 (mmt) cc_final: 0.7982 (mmm) REVERT: C 339 TYR cc_start: 0.8604 (m-80) cc_final: 0.8312 (m-10) REVERT: D 123 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8394 (tt0) REVERT: D 215 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8728 (tttp) REVERT: E 23 PHE cc_start: 0.8171 (m-80) cc_final: 0.7826 (m-80) REVERT: E 134 MET cc_start: 0.7831 (pmm) cc_final: 0.7495 (pmm) REVERT: E 191 LEU cc_start: 0.9010 (tp) cc_final: 0.8804 (tp) REVERT: E 193 LYS cc_start: 0.8979 (ttmt) cc_final: 0.8742 (ttmm) REVERT: E 209 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8645 (mm-30) REVERT: E 228 GLU cc_start: 0.8664 (tp30) cc_final: 0.8311 (tp30) REVERT: E 258 ARG cc_start: 0.9155 (mtm-85) cc_final: 0.7993 (ttm110) REVERT: E 298 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7498 (t0) outliers start: 68 outliers final: 50 residues processed: 571 average time/residue: 0.2603 time to fit residues: 219.3041 Evaluate side-chains 558 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 504 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 299 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 46 optimal weight: 4.9990 chunk 164 optimal weight: 0.0170 chunk 43 optimal weight: 0.0980 chunk 147 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 105 optimal weight: 0.0980 chunk 179 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 173 optimal weight: 0.5980 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN C 117 ASN C 254 ASN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.114782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.098499 restraints weight = 31071.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.101859 restraints weight = 15765.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.104157 restraints weight = 9600.807| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14910 Z= 0.206 Angle : 0.695 8.083 20230 Z= 0.334 Chirality : 0.046 0.171 2230 Planarity : 0.005 0.069 2590 Dihedral : 9.844 175.719 2078 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.31 % Allowed : 27.07 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.20), residues: 1840 helix: -0.10 (0.19), residues: 750 sheet: 0.34 (0.29), residues: 340 loop : 0.27 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 342 HIS 0.005 0.001 HIS A 90 PHE 0.012 0.001 PHE E 354 TYR 0.021 0.002 TYR A 168 ARG 0.007 0.001 ARG E 212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 552 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.7809 (tp-100) cc_final: 0.7317 (tp-100) REVERT: A 103 HIS cc_start: 0.8446 (m90) cc_final: 0.7892 (m90) REVERT: A 113 ASN cc_start: 0.8991 (t0) cc_final: 0.8584 (t0) REVERT: A 142 LEU cc_start: 0.9214 (mt) cc_final: 0.8801 (mt) REVERT: A 145 TYR cc_start: 0.8027 (m-80) cc_final: 0.7744 (m-10) REVERT: A 212 ARG cc_start: 0.8536 (ttp80) cc_final: 0.8223 (tmm-80) REVERT: A 224 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.7957 (p0) REVERT: B 64 ARG cc_start: 0.9266 (ptt180) cc_final: 0.8677 (ptm160) REVERT: B 84 MET cc_start: 0.8450 (tpp) cc_final: 0.7264 (tpp) REVERT: B 88 TRP cc_start: 0.9367 (m-10) cc_final: 0.8790 (m-90) REVERT: B 119 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8647 (mt-10) REVERT: B 134 MET cc_start: 0.8923 (ppp) cc_final: 0.8603 (tmm) REVERT: B 169 GLU cc_start: 0.8854 (mp0) cc_final: 0.8420 (mm-30) REVERT: B 208 ARG cc_start: 0.8392 (ttp80) cc_final: 0.8131 (ttm-80) REVERT: B 223 LEU cc_start: 0.9084 (tt) cc_final: 0.8770 (tp) REVERT: B 272 GLU cc_start: 0.7419 (tt0) cc_final: 0.7119 (tt0) REVERT: B 294 ASP cc_start: 0.8518 (m-30) cc_final: 0.8191 (t0) REVERT: B 313 ASP cc_start: 0.8288 (t70) cc_final: 0.8036 (t0) REVERT: B 316 GLN cc_start: 0.9142 (tm-30) cc_final: 0.8622 (tm-30) REVERT: B 331 MET cc_start: 0.8211 (mtt) cc_final: 0.7773 (mtt) REVERT: C 118 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8577 (mtm180) REVERT: C 254 ASN cc_start: 0.8919 (OUTLIER) cc_final: 0.8466 (p0) REVERT: C 286 LYS cc_start: 0.8937 (ttmm) cc_final: 0.8595 (mtpp) REVERT: C 327 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7797 (mmm) REVERT: C 339 TYR cc_start: 0.8556 (m-80) cc_final: 0.8275 (m-10) REVERT: D 30 ARG cc_start: 0.7529 (mmm-85) cc_final: 0.7027 (mtp-110) REVERT: D 80 ASN cc_start: 0.8372 (t0) cc_final: 0.8145 (t0) REVERT: D 118 ARG cc_start: 0.8691 (ptt-90) cc_final: 0.8181 (ptt-90) REVERT: D 123 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8511 (tt0) REVERT: E 193 LYS cc_start: 0.8970 (ttmt) cc_final: 0.8693 (ttmm) REVERT: E 212 ARG cc_start: 0.8715 (ttp80) cc_final: 0.8438 (ttp80) REVERT: E 228 GLU cc_start: 0.8713 (tp30) cc_final: 0.8286 (tp30) REVERT: E 258 ARG cc_start: 0.9121 (mtm-85) cc_final: 0.7993 (ttm110) REVERT: E 316 GLN cc_start: 0.8546 (tp40) cc_final: 0.8124 (tp40) outliers start: 67 outliers final: 49 residues processed: 582 average time/residue: 0.2514 time to fit residues: 219.6469 Evaluate side-chains 554 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 500 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 327 MET Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 305 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 88 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 168 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 169 optimal weight: 0.0770 chunk 149 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.1140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN B 90 HIS ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 ASN E 14 ASN E 61 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN E 355 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.096443 restraints weight = 31224.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.099678 restraints weight = 15792.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.101889 restraints weight = 9571.508| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14910 Z= 0.235 Angle : 0.698 9.898 20230 Z= 0.334 Chirality : 0.046 0.176 2230 Planarity : 0.005 0.060 2590 Dihedral : 9.653 174.990 2078 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 5.59 % Allowed : 26.43 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.20), residues: 1840 helix: -0.07 (0.19), residues: 755 sheet: 0.35 (0.29), residues: 340 loop : 0.33 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 342 HIS 0.007 0.001 HIS B 373 PHE 0.011 0.001 PHE E 257 TYR 0.021 0.001 TYR A 168 ARG 0.007 0.001 ARG E 212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 535 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.7865 (tp-100) cc_final: 0.7366 (tp-100) REVERT: A 70 LYS cc_start: 0.8781 (mmmm) cc_final: 0.8357 (mmmm) REVERT: A 103 HIS cc_start: 0.8456 (m90) cc_final: 0.7890 (m90) REVERT: A 145 TYR cc_start: 0.8017 (m-80) cc_final: 0.7784 (m-10) REVERT: A 212 ARG cc_start: 0.8487 (ttp80) cc_final: 0.8192 (tmm-80) REVERT: A 354 PHE cc_start: 0.8748 (t80) cc_final: 0.8417 (t80) REVERT: B 84 MET cc_start: 0.8625 (tpp) cc_final: 0.7367 (tpp) REVERT: B 88 TRP cc_start: 0.9355 (OUTLIER) cc_final: 0.8783 (m-90) REVERT: B 113 ASN cc_start: 0.9323 (t0) cc_final: 0.8867 (t0) REVERT: B 123 GLN cc_start: 0.9290 (tt0) cc_final: 0.8769 (tp-100) REVERT: B 169 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8316 (mm-30) REVERT: B 208 ARG cc_start: 0.8375 (ttp80) cc_final: 0.8107 (ttm-80) REVERT: B 223 LEU cc_start: 0.9049 (tt) cc_final: 0.8730 (tp) REVERT: B 272 GLU cc_start: 0.7517 (tt0) cc_final: 0.7173 (tt0) REVERT: B 294 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8189 (t0) REVERT: B 313 ASP cc_start: 0.8276 (t70) cc_final: 0.8015 (t0) REVERT: B 316 GLN cc_start: 0.9154 (tm-30) cc_final: 0.8403 (tm-30) REVERT: B 358 TRP cc_start: 0.8098 (m-90) cc_final: 0.7606 (m-90) REVERT: C 12 CYS cc_start: 0.8792 (t) cc_final: 0.8357 (t) REVERT: C 61 GLN cc_start: 0.8326 (tp-100) cc_final: 0.7989 (tp40) REVERT: C 118 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8572 (mtm180) REVERT: C 248 GLN cc_start: 0.8774 (tt0) cc_final: 0.8134 (mt0) REVERT: C 254 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8388 (p0) REVERT: C 286 LYS cc_start: 0.8964 (ttmm) cc_final: 0.8628 (mtpp) REVERT: C 288 ASP cc_start: 0.8096 (m-30) cc_final: 0.7827 (m-30) REVERT: C 298 ASN cc_start: 0.8509 (m-40) cc_final: 0.7562 (t0) REVERT: C 327 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7857 (mmm) REVERT: C 358 TRP cc_start: 0.8706 (m100) cc_final: 0.8249 (m100) REVERT: D 80 ASN cc_start: 0.8500 (t0) cc_final: 0.8220 (t0) REVERT: D 118 ARG cc_start: 0.8774 (ptt-90) cc_final: 0.8263 (ptt-90) REVERT: D 123 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8435 (tt0) REVERT: D 316 GLN cc_start: 0.8374 (tm-30) cc_final: 0.7979 (tm-30) REVERT: E 122 THR cc_start: 0.8718 (m) cc_final: 0.8337 (t) REVERT: E 126 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.8008 (m-10) REVERT: E 191 LEU cc_start: 0.9066 (tp) cc_final: 0.8840 (tt) REVERT: E 193 LYS cc_start: 0.8966 (ttmt) cc_final: 0.8689 (ttmm) REVERT: E 228 GLU cc_start: 0.8765 (tp30) cc_final: 0.8371 (tp30) REVERT: E 258 ARG cc_start: 0.9115 (mtm-85) cc_final: 0.7990 (ttm110) REVERT: E 298 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.7859 (t0) REVERT: E 316 GLN cc_start: 0.8565 (tp40) cc_final: 0.8037 (tp40) outliers start: 87 outliers final: 63 residues processed: 567 average time/residue: 0.2393 time to fit residues: 206.2698 Evaluate side-chains 571 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 499 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 88 TRP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 355 GLN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 327 MET Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 305 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 127 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 31 optimal weight: 0.2980 chunk 0 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 175 optimal weight: 0.0980 chunk 150 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN B 90 HIS ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 ASN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 ASN D 355 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.096258 restraints weight = 31651.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.099523 restraints weight = 15981.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.101778 restraints weight = 9686.549| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14910 Z= 0.222 Angle : 0.685 8.925 20230 Z= 0.327 Chirality : 0.046 0.149 2230 Planarity : 0.005 0.059 2590 Dihedral : 9.547 173.517 2078 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 5.92 % Allowed : 26.37 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.20), residues: 1840 helix: -0.01 (0.19), residues: 755 sheet: 0.54 (0.30), residues: 325 loop : 0.37 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 342 HIS 0.010 0.001 HIS B 373 PHE 0.010 0.001 PHE E 354 TYR 0.022 0.001 TYR A 168 ARG 0.006 0.001 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 531 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.7954 (tp-100) cc_final: 0.7486 (tp-100) REVERT: A 70 LYS cc_start: 0.8761 (mmmm) cc_final: 0.8341 (mmmm) REVERT: A 103 HIS cc_start: 0.8460 (m90) cc_final: 0.7998 (m90) REVERT: A 212 ARG cc_start: 0.8466 (ttp80) cc_final: 0.8192 (tmm-80) REVERT: A 224 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.7962 (p0) REVERT: B 84 MET cc_start: 0.8702 (tpp) cc_final: 0.7453 (tpp) REVERT: B 88 TRP cc_start: 0.9358 (OUTLIER) cc_final: 0.8783 (m-90) REVERT: B 113 ASN cc_start: 0.9330 (t0) cc_final: 0.8986 (t0) REVERT: B 119 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8587 (mt-10) REVERT: B 123 GLN cc_start: 0.9262 (tt0) cc_final: 0.8921 (tp40) REVERT: B 169 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8276 (mm-30) REVERT: B 179 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.6565 (ttm170) REVERT: B 208 ARG cc_start: 0.8367 (ttp80) cc_final: 0.8129 (ttm-80) REVERT: B 272 GLU cc_start: 0.7501 (tt0) cc_final: 0.7118 (tt0) REVERT: B 281 TYR cc_start: 0.8877 (t80) cc_final: 0.8288 (t80) REVERT: B 294 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8179 (t0) REVERT: B 307 MET cc_start: 0.8559 (mtp) cc_final: 0.8322 (mtp) REVERT: B 316 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8610 (tm-30) REVERT: B 357 MET cc_start: 0.8586 (mmm) cc_final: 0.8219 (mtp) REVERT: C 12 CYS cc_start: 0.8789 (t) cc_final: 0.8157 (t) REVERT: C 14 ASN cc_start: 0.7832 (m110) cc_final: 0.7068 (m-40) REVERT: C 123 GLN cc_start: 0.8615 (tt0) cc_final: 0.8237 (tm-30) REVERT: C 248 GLN cc_start: 0.8760 (tt0) cc_final: 0.8088 (mt0) REVERT: C 254 ASN cc_start: 0.8798 (OUTLIER) cc_final: 0.8361 (p0) REVERT: C 288 ASP cc_start: 0.8168 (m-30) cc_final: 0.7865 (m-30) REVERT: C 298 ASN cc_start: 0.8445 (m-40) cc_final: 0.7579 (t0) REVERT: C 327 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7849 (mmm) REVERT: C 342 TRP cc_start: 0.8031 (t60) cc_final: 0.7150 (t60) REVERT: C 358 TRP cc_start: 0.8709 (m100) cc_final: 0.8284 (m100) REVERT: D 30 ARG cc_start: 0.7533 (mmm-85) cc_final: 0.7021 (mtp-110) REVERT: D 80 ASN cc_start: 0.8498 (t0) cc_final: 0.8182 (t0) REVERT: D 115 LYS cc_start: 0.8303 (mmtt) cc_final: 0.7655 (ptpp) REVERT: D 118 ARG cc_start: 0.8769 (ptt-90) cc_final: 0.8205 (ptt-90) REVERT: D 316 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8091 (tm-30) REVERT: E 30 ARG cc_start: 0.8384 (mmp80) cc_final: 0.8020 (mmm160) REVERT: E 122 THR cc_start: 0.8756 (m) cc_final: 0.8386 (t) REVERT: E 125 MET cc_start: 0.9140 (mmp) cc_final: 0.8814 (mmp) REVERT: E 126 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.7953 (m-10) REVERT: E 191 LEU cc_start: 0.9052 (tp) cc_final: 0.8821 (tt) REVERT: E 193 LYS cc_start: 0.8968 (ttmt) cc_final: 0.8688 (ttmm) REVERT: E 228 GLU cc_start: 0.8799 (tp30) cc_final: 0.8434 (tp30) REVERT: E 298 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.7793 (t0) REVERT: E 316 GLN cc_start: 0.8598 (tp40) cc_final: 0.8033 (tp40) outliers start: 92 outliers final: 63 residues processed: 567 average time/residue: 0.2358 time to fit residues: 202.5088 Evaluate side-chains 573 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 501 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 88 TRP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 355 GLN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 327 MET Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 305 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 99 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 132 optimal weight: 0.0870 chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN B 90 HIS ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 ASN E 14 ASN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.098323 restraints weight = 31046.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.101633 restraints weight = 15675.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.103925 restraints weight = 9513.396| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14910 Z= 0.190 Angle : 0.683 8.009 20230 Z= 0.326 Chirality : 0.046 0.181 2230 Planarity : 0.005 0.058 2590 Dihedral : 9.441 174.451 2078 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.14 % Allowed : 27.01 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.20), residues: 1840 helix: 0.09 (0.20), residues: 750 sheet: 0.56 (0.29), residues: 325 loop : 0.36 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 342 HIS 0.009 0.001 HIS B 373 PHE 0.033 0.001 PHE A 354 TYR 0.019 0.001 TYR A 145 ARG 0.006 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 547 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8112 (tp-100) cc_final: 0.7755 (tp-100) REVERT: A 70 LYS cc_start: 0.8746 (mmmm) cc_final: 0.8314 (mmmm) REVERT: A 103 HIS cc_start: 0.8492 (m90) cc_final: 0.8036 (m90) REVERT: A 212 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8141 (tmm-80) REVERT: A 354 PHE cc_start: 0.8721 (t80) cc_final: 0.8258 (t80) REVERT: B 113 ASN cc_start: 0.9314 (t0) cc_final: 0.8939 (t0) REVERT: B 115 LYS cc_start: 0.9014 (mmmt) cc_final: 0.8731 (mmmt) REVERT: B 119 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8632 (mt-10) REVERT: B 123 GLN cc_start: 0.9271 (tt0) cc_final: 0.8836 (tp40) REVERT: B 169 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8161 (mm-30) REVERT: B 179 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.6550 (ttm170) REVERT: B 208 ARG cc_start: 0.8323 (ttp80) cc_final: 0.8098 (ttm-80) REVERT: B 272 GLU cc_start: 0.7529 (tt0) cc_final: 0.7197 (tt0) REVERT: B 281 TYR cc_start: 0.8832 (t80) cc_final: 0.8334 (t80) REVERT: B 294 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8158 (t0) REVERT: B 307 MET cc_start: 0.8548 (mtp) cc_final: 0.8324 (mtp) REVERT: B 316 GLN cc_start: 0.8685 (tm-30) cc_final: 0.8474 (tm-30) REVERT: B 357 MET cc_start: 0.8649 (mmm) cc_final: 0.8262 (mtp) REVERT: C 123 GLN cc_start: 0.8624 (tt0) cc_final: 0.8319 (tm-30) REVERT: C 169 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8103 (mm-30) REVERT: C 248 GLN cc_start: 0.8742 (tt0) cc_final: 0.8110 (mt0) REVERT: C 255 GLU cc_start: 0.8855 (pm20) cc_final: 0.8419 (pm20) REVERT: C 288 ASP cc_start: 0.8181 (m-30) cc_final: 0.7882 (m-30) REVERT: C 298 ASN cc_start: 0.8409 (m-40) cc_final: 0.7602 (t0) REVERT: C 316 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8410 (tm-30) REVERT: C 327 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7671 (mmm) REVERT: C 339 TYR cc_start: 0.8503 (m-80) cc_final: 0.8060 (m-80) REVERT: C 342 TRP cc_start: 0.7957 (t60) cc_final: 0.7161 (t60) REVERT: D 30 ARG cc_start: 0.7565 (mmm-85) cc_final: 0.7056 (mtp-110) REVERT: D 80 ASN cc_start: 0.8451 (t0) cc_final: 0.8108 (t0) REVERT: D 115 LYS cc_start: 0.8194 (mmtt) cc_final: 0.7472 (ptpp) REVERT: D 118 ARG cc_start: 0.8760 (ptt-90) cc_final: 0.8208 (ptt-90) REVERT: D 254 ASN cc_start: 0.9392 (p0) cc_final: 0.8824 (p0) REVERT: D 316 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7925 (tm-30) REVERT: D 331 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8227 (mtm) REVERT: D 354 PHE cc_start: 0.8176 (t80) cc_final: 0.7793 (t80) REVERT: E 30 ARG cc_start: 0.8403 (mmp80) cc_final: 0.8180 (mmp-170) REVERT: E 46 MET cc_start: 0.7764 (tpp) cc_final: 0.7058 (tpp) REVERT: E 126 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7919 (m-10) REVERT: E 159 ASP cc_start: 0.8542 (t0) cc_final: 0.8314 (t0) REVERT: E 173 LEU cc_start: 0.8946 (mt) cc_final: 0.8718 (mt) REVERT: E 191 LEU cc_start: 0.9018 (tp) cc_final: 0.8686 (tt) REVERT: E 193 LYS cc_start: 0.8954 (ttmt) cc_final: 0.8691 (ttmm) REVERT: E 228 GLU cc_start: 0.8773 (tp30) cc_final: 0.8466 (tp30) REVERT: E 290 ASP cc_start: 0.6894 (p0) cc_final: 0.6390 (p0) REVERT: E 298 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.7853 (t0) REVERT: E 316 GLN cc_start: 0.8631 (tp40) cc_final: 0.8030 (tp40) outliers start: 80 outliers final: 59 residues processed: 575 average time/residue: 0.2359 time to fit residues: 206.9638 Evaluate side-chains 579 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 513 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 88 TRP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 355 GLN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 327 MET Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 305 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 25 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 179 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 162 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN B 90 HIS ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 GLN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 GLN E 43 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.110454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.094728 restraints weight = 32018.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.097987 restraints weight = 16206.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.100209 restraints weight = 9841.424| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14910 Z= 0.261 Angle : 0.711 8.399 20230 Z= 0.343 Chirality : 0.047 0.166 2230 Planarity : 0.005 0.056 2590 Dihedral : 9.438 171.903 2078 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 5.98 % Allowed : 27.27 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.20), residues: 1840 helix: 0.13 (0.20), residues: 750 sheet: 0.52 (0.30), residues: 325 loop : 0.34 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 342 HIS 0.009 0.001 HIS B 373 PHE 0.026 0.002 PHE E 225 TYR 0.016 0.001 TYR A 168 ARG 0.005 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 521 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8189 (tp-100) cc_final: 0.7804 (tp-100) REVERT: A 70 LYS cc_start: 0.8781 (mmmm) cc_final: 0.8362 (mmmm) REVERT: A 103 HIS cc_start: 0.8514 (m90) cc_final: 0.8061 (m90) REVERT: A 127 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7547 (tm-30) REVERT: A 212 ARG cc_start: 0.8464 (ttp80) cc_final: 0.8157 (tmm-80) REVERT: A 224 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8429 (p0) REVERT: B 88 TRP cc_start: 0.9337 (m-10) cc_final: 0.8827 (m-90) REVERT: B 113 ASN cc_start: 0.9347 (t0) cc_final: 0.8946 (t0) REVERT: B 115 LYS cc_start: 0.9025 (mmmt) cc_final: 0.8714 (mmmt) REVERT: B 119 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8600 (mt-10) REVERT: B 123 GLN cc_start: 0.9302 (tt0) cc_final: 0.8829 (tp40) REVERT: B 149 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.6714 (mpp80) REVERT: B 169 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8163 (mm-30) REVERT: B 179 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.6632 (ttm170) REVERT: B 208 ARG cc_start: 0.8397 (ttp80) cc_final: 0.8108 (ttm-80) REVERT: B 272 GLU cc_start: 0.7531 (tt0) cc_final: 0.7193 (tt0) REVERT: B 281 TYR cc_start: 0.8850 (t80) cc_final: 0.8299 (t80) REVERT: B 294 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8263 (t0) REVERT: B 316 GLN cc_start: 0.8840 (tm-30) cc_final: 0.8434 (tm-30) REVERT: B 357 MET cc_start: 0.8657 (mmm) cc_final: 0.7836 (mmm) REVERT: C 12 CYS cc_start: 0.8845 (t) cc_final: 0.8331 (t) REVERT: C 123 GLN cc_start: 0.8651 (tt0) cc_final: 0.8324 (tm-30) REVERT: C 248 GLN cc_start: 0.8782 (tt0) cc_final: 0.8079 (mt0) REVERT: C 255 GLU cc_start: 0.9029 (pm20) cc_final: 0.8792 (pm20) REVERT: C 288 ASP cc_start: 0.8269 (m-30) cc_final: 0.7952 (m-30) REVERT: C 316 GLN cc_start: 0.8917 (tm-30) cc_final: 0.8431 (tm-30) REVERT: C 327 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7655 (mmm) REVERT: C 342 TRP cc_start: 0.8018 (t60) cc_final: 0.7214 (t60) REVERT: D 30 ARG cc_start: 0.7639 (mmm-85) cc_final: 0.7139 (mtp-110) REVERT: D 80 ASN cc_start: 0.8504 (t0) cc_final: 0.8156 (t0) REVERT: D 115 LYS cc_start: 0.8275 (mmtt) cc_final: 0.7572 (ptpp) REVERT: D 118 ARG cc_start: 0.8772 (ptt-90) cc_final: 0.8414 (ptt-90) REVERT: D 316 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7978 (tm-30) REVERT: E 30 ARG cc_start: 0.8569 (mmp80) cc_final: 0.8152 (mmp-170) REVERT: E 43 GLN cc_start: 0.8262 (tp-100) cc_final: 0.7902 (tp-100) REVERT: E 122 THR cc_start: 0.8789 (m) cc_final: 0.8436 (t) REVERT: E 126 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.8023 (m-10) REVERT: E 193 LYS cc_start: 0.8977 (ttmt) cc_final: 0.8719 (ttmm) REVERT: E 228 GLU cc_start: 0.8767 (tp30) cc_final: 0.8399 (tp30) REVERT: E 278 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7069 (tm-30) REVERT: E 298 ASN cc_start: 0.8362 (OUTLIER) cc_final: 0.7891 (t0) REVERT: E 316 GLN cc_start: 0.8651 (tp40) cc_final: 0.7991 (tp40) outliers start: 93 outliers final: 73 residues processed: 553 average time/residue: 0.2336 time to fit residues: 197.4045 Evaluate side-chains 564 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 483 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 355 GLN Chi-restraints excluded: chain B residue 373 HIS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 327 MET Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 305 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 121 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 167 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 73 optimal weight: 0.2980 chunk 149 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 77 optimal weight: 0.0010 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.113332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.097585 restraints weight = 30927.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.100860 restraints weight = 15631.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.103133 restraints weight = 9478.551| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14910 Z= 0.189 Angle : 0.717 10.133 20230 Z= 0.341 Chirality : 0.046 0.161 2230 Planarity : 0.005 0.056 2590 Dihedral : 9.256 172.923 2075 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.18 % Allowed : 29.13 % Favored : 66.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.20), residues: 1840 helix: 0.19 (0.20), residues: 750 sheet: 0.58 (0.29), residues: 325 loop : 0.36 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 342 HIS 0.009 0.001 HIS D 175 PHE 0.047 0.001 PHE A 354 TYR 0.027 0.001 TYR C 168 ARG 0.006 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 541 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8190 (tp-100) cc_final: 0.7846 (tp-100) REVERT: A 70 LYS cc_start: 0.8762 (mmmm) cc_final: 0.8340 (mmmm) REVERT: A 103 HIS cc_start: 0.8531 (m90) cc_final: 0.8065 (m90) REVERT: A 127 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7606 (tm-30) REVERT: A 212 ARG cc_start: 0.8402 (ttp80) cc_final: 0.8112 (tmm-80) REVERT: B 83 ASP cc_start: 0.8577 (m-30) cc_final: 0.8331 (p0) REVERT: B 88 TRP cc_start: 0.9232 (OUTLIER) cc_final: 0.8824 (m-90) REVERT: B 113 ASN cc_start: 0.9326 (t0) cc_final: 0.9116 (t0) REVERT: B 119 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8614 (mt-10) REVERT: B 123 GLN cc_start: 0.9247 (tt0) cc_final: 0.8704 (tp-100) REVERT: B 149 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.6749 (mpp80) REVERT: B 169 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8124 (mm-30) REVERT: B 272 GLU cc_start: 0.7579 (tt0) cc_final: 0.7224 (tt0) REVERT: B 281 TYR cc_start: 0.8804 (t80) cc_final: 0.8339 (t80) REVERT: B 294 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8250 (t0) REVERT: B 316 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8391 (tm-30) REVERT: B 331 MET cc_start: 0.8376 (mtm) cc_final: 0.7863 (mtm) REVERT: B 357 MET cc_start: 0.8694 (mmm) cc_final: 0.7814 (mmm) REVERT: C 12 CYS cc_start: 0.8839 (t) cc_final: 0.8359 (t) REVERT: C 123 GLN cc_start: 0.8574 (tt0) cc_final: 0.8314 (tm-30) REVERT: C 169 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8112 (mp0) REVERT: C 248 GLN cc_start: 0.8779 (tt0) cc_final: 0.8121 (mt0) REVERT: C 288 ASP cc_start: 0.8199 (m-30) cc_final: 0.7920 (m-30) REVERT: C 316 GLN cc_start: 0.8885 (tm-30) cc_final: 0.8382 (tm-30) REVERT: C 327 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7568 (mmm) REVERT: C 339 TYR cc_start: 0.8539 (m-80) cc_final: 0.8198 (m-80) REVERT: C 342 TRP cc_start: 0.7934 (t60) cc_final: 0.7028 (t60) REVERT: D 30 ARG cc_start: 0.7549 (mmm-85) cc_final: 0.6969 (mtp-110) REVERT: D 80 ASN cc_start: 0.8493 (t0) cc_final: 0.8129 (t0) REVERT: D 115 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7380 (ptpp) REVERT: D 118 ARG cc_start: 0.8749 (ptt-90) cc_final: 0.8351 (ptt-90) REVERT: D 318 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8718 (mm-30) REVERT: E 30 ARG cc_start: 0.8533 (mmp80) cc_final: 0.8035 (mmp-170) REVERT: E 43 GLN cc_start: 0.8251 (tp-100) cc_final: 0.7884 (tp-100) REVERT: E 113 ASN cc_start: 0.8713 (t0) cc_final: 0.8451 (t0) REVERT: E 122 THR cc_start: 0.8768 (m) cc_final: 0.8413 (t) REVERT: E 126 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7918 (m-10) REVERT: E 193 LYS cc_start: 0.8955 (ttmt) cc_final: 0.8714 (ttmm) REVERT: E 228 GLU cc_start: 0.8751 (tp30) cc_final: 0.8418 (tp30) REVERT: E 278 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7118 (tm-30) REVERT: E 298 ASN cc_start: 0.8358 (OUTLIER) cc_final: 0.7963 (t0) REVERT: E 316 GLN cc_start: 0.8631 (tp40) cc_final: 0.7874 (tp40) outliers start: 65 outliers final: 53 residues processed: 561 average time/residue: 0.2320 time to fit residues: 198.5991 Evaluate side-chains 568 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 508 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 88 TRP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 355 GLN Chi-restraints excluded: chain B residue 373 HIS Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 327 MET Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 305 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 34 optimal weight: 7.9990 chunk 92 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 168 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN B 90 HIS ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN E 373 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.112939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.097348 restraints weight = 31067.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.100598 restraints weight = 15813.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.102767 restraints weight = 9618.763| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14910 Z= 0.217 Angle : 0.730 10.421 20230 Z= 0.348 Chirality : 0.046 0.190 2230 Planarity : 0.005 0.056 2590 Dihedral : 9.220 174.871 2075 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.69 % Allowed : 28.87 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.20), residues: 1840 helix: 0.19 (0.20), residues: 750 sheet: 0.57 (0.29), residues: 325 loop : 0.36 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 342 HIS 0.008 0.001 HIS D 175 PHE 0.050 0.001 PHE A 354 TYR 0.015 0.001 TYR D 55 ARG 0.007 0.001 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 524 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8209 (tp-100) cc_final: 0.7879 (tp-100) REVERT: A 70 LYS cc_start: 0.8758 (mmmm) cc_final: 0.8396 (mmmm) REVERT: A 103 HIS cc_start: 0.8533 (m90) cc_final: 0.8060 (m90) REVERT: A 127 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7567 (tm-30) REVERT: A 212 ARG cc_start: 0.8437 (ttp80) cc_final: 0.8132 (tmm-80) REVERT: A 354 PHE cc_start: 0.8701 (t80) cc_final: 0.8364 (t80) REVERT: B 83 ASP cc_start: 0.8667 (m-30) cc_final: 0.8409 (p0) REVERT: B 88 TRP cc_start: 0.9264 (OUTLIER) cc_final: 0.8842 (m-90) REVERT: B 113 ASN cc_start: 0.9368 (t0) cc_final: 0.9040 (t0) REVERT: B 119 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8605 (mt-10) REVERT: B 123 GLN cc_start: 0.9256 (tt0) cc_final: 0.8827 (tp40) REVERT: B 149 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.6918 (mpp80) REVERT: B 169 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8124 (mm-30) REVERT: B 272 GLU cc_start: 0.7557 (tt0) cc_final: 0.7110 (tt0) REVERT: B 281 TYR cc_start: 0.8812 (t80) cc_final: 0.8361 (t80) REVERT: B 294 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8251 (t0) REVERT: B 316 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8324 (tm-30) REVERT: B 357 MET cc_start: 0.8695 (mmm) cc_final: 0.7790 (mmm) REVERT: C 12 CYS cc_start: 0.8842 (t) cc_final: 0.8361 (t) REVERT: C 123 GLN cc_start: 0.8585 (tt0) cc_final: 0.8323 (tm-30) REVERT: C 168 TYR cc_start: 0.8182 (t80) cc_final: 0.7725 (t80) REVERT: C 169 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7990 (mm-30) REVERT: C 171 TYR cc_start: 0.8306 (m-10) cc_final: 0.8033 (m-10) REVERT: C 248 GLN cc_start: 0.8775 (tt0) cc_final: 0.8108 (mt0) REVERT: C 288 ASP cc_start: 0.8182 (m-30) cc_final: 0.7912 (m-30) REVERT: C 298 ASN cc_start: 0.8424 (m-40) cc_final: 0.7553 (t0) REVERT: C 339 TYR cc_start: 0.8576 (m-80) cc_final: 0.8205 (m-80) REVERT: C 342 TRP cc_start: 0.7894 (t60) cc_final: 0.6959 (t60) REVERT: D 30 ARG cc_start: 0.7544 (mmm-85) cc_final: 0.7000 (mtp-110) REVERT: D 80 ASN cc_start: 0.8499 (t0) cc_final: 0.8123 (t0) REVERT: D 115 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7370 (ptpp) REVERT: D 118 ARG cc_start: 0.8803 (ptt-90) cc_final: 0.8069 (ptt-90) REVERT: D 316 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7734 (tm-30) REVERT: D 318 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8726 (mm-30) REVERT: E 30 ARG cc_start: 0.8575 (mmp80) cc_final: 0.8125 (mmp-170) REVERT: E 43 GLN cc_start: 0.8300 (tp-100) cc_final: 0.7944 (tp-100) REVERT: E 122 THR cc_start: 0.8757 (m) cc_final: 0.8417 (t) REVERT: E 126 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7993 (m-10) REVERT: E 169 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8708 (mm-30) REVERT: E 191 LEU cc_start: 0.8965 (tp) cc_final: 0.8670 (tt) REVERT: E 193 LYS cc_start: 0.8943 (ttmt) cc_final: 0.8650 (ttmm) REVERT: E 228 GLU cc_start: 0.8754 (tp30) cc_final: 0.8428 (tp30) REVERT: E 272 GLU cc_start: 0.5014 (pt0) cc_final: 0.4080 (tt0) REVERT: E 278 GLU cc_start: 0.8443 (tm-30) cc_final: 0.7220 (tm-30) REVERT: E 292 ARG cc_start: 0.8647 (mtt180) cc_final: 0.7347 (ptt180) REVERT: E 298 ASN cc_start: 0.8366 (OUTLIER) cc_final: 0.7948 (t0) REVERT: E 316 GLN cc_start: 0.8656 (tp40) cc_final: 0.8067 (tp40) outliers start: 73 outliers final: 62 residues processed: 546 average time/residue: 0.2381 time to fit residues: 197.4258 Evaluate side-chains 581 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 513 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 88 TRP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 355 GLN Chi-restraints excluded: chain B residue 373 HIS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 305 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 114 optimal weight: 0.5980 chunk 116 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 173 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.113724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.098160 restraints weight = 31062.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.101415 restraints weight = 15793.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.103606 restraints weight = 9596.365| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14910 Z= 0.210 Angle : 0.748 10.940 20230 Z= 0.355 Chirality : 0.046 0.190 2230 Planarity : 0.005 0.056 2590 Dihedral : 9.187 179.617 2075 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.57 % Allowed : 29.52 % Favored : 65.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.20), residues: 1840 helix: 0.17 (0.20), residues: 750 sheet: 0.57 (0.29), residues: 325 loop : 0.37 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 342 HIS 0.014 0.001 HIS E 373 PHE 0.042 0.001 PHE A 354 TYR 0.032 0.002 TYR A 145 ARG 0.007 0.001 ARG B 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 532 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8185 (tp-100) cc_final: 0.7905 (tp-100) REVERT: A 70 LYS cc_start: 0.8760 (mmmm) cc_final: 0.8408 (mmmm) REVERT: A 103 HIS cc_start: 0.8521 (m90) cc_final: 0.8048 (m90) REVERT: A 127 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7583 (tm-30) REVERT: A 212 ARG cc_start: 0.8429 (ttp80) cc_final: 0.8075 (tmm-80) REVERT: A 331 MET cc_start: 0.8257 (mtm) cc_final: 0.7988 (mtm) REVERT: B 83 ASP cc_start: 0.8633 (m-30) cc_final: 0.8385 (p0) REVERT: B 88 TRP cc_start: 0.9238 (OUTLIER) cc_final: 0.8828 (m-90) REVERT: B 119 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8583 (mt-10) REVERT: B 123 GLN cc_start: 0.9234 (tt0) cc_final: 0.8813 (tp40) REVERT: B 149 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.6799 (mpp80) REVERT: B 169 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8105 (mm-30) REVERT: B 272 GLU cc_start: 0.7631 (tt0) cc_final: 0.7209 (tt0) REVERT: B 281 TYR cc_start: 0.8799 (t80) cc_final: 0.8368 (t80) REVERT: B 294 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8240 (t0) REVERT: B 316 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8335 (tm-30) REVERT: B 357 MET cc_start: 0.8664 (mmm) cc_final: 0.7729 (mmm) REVERT: C 12 CYS cc_start: 0.8830 (t) cc_final: 0.8370 (t) REVERT: C 123 GLN cc_start: 0.8553 (tt0) cc_final: 0.8296 (tm-30) REVERT: C 248 GLN cc_start: 0.8759 (tt0) cc_final: 0.8104 (mt0) REVERT: C 288 ASP cc_start: 0.8207 (m-30) cc_final: 0.7933 (m-30) REVERT: C 316 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8455 (tm-30) REVERT: C 339 TYR cc_start: 0.8531 (m-80) cc_final: 0.8226 (m-80) REVERT: C 342 TRP cc_start: 0.7884 (t60) cc_final: 0.6951 (t60) REVERT: D 30 ARG cc_start: 0.7465 (mmm-85) cc_final: 0.6919 (mtp-110) REVERT: D 80 ASN cc_start: 0.8478 (t0) cc_final: 0.8118 (t0) REVERT: D 115 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7287 (ptpp) REVERT: D 118 ARG cc_start: 0.8803 (ptt-90) cc_final: 0.8109 (ptt-90) REVERT: D 316 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7591 (tm-30) REVERT: D 318 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8715 (mm-30) REVERT: E 30 ARG cc_start: 0.8582 (mmp80) cc_final: 0.8149 (mmp-170) REVERT: E 43 GLN cc_start: 0.8273 (tp-100) cc_final: 0.7921 (tp-100) REVERT: E 46 MET cc_start: 0.7885 (tpp) cc_final: 0.7099 (tpp) REVERT: E 122 THR cc_start: 0.8694 (m) cc_final: 0.8341 (t) REVERT: E 126 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7996 (m-10) REVERT: E 169 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8697 (mm-30) REVERT: E 193 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8658 (ttmm) REVERT: E 228 GLU cc_start: 0.8711 (tp30) cc_final: 0.8408 (tp30) REVERT: E 272 GLU cc_start: 0.5073 (pt0) cc_final: 0.4108 (tt0) REVERT: E 278 GLU cc_start: 0.8426 (tm-30) cc_final: 0.7187 (tm-30) REVERT: E 292 ARG cc_start: 0.8672 (mtt180) cc_final: 0.7342 (ptt180) REVERT: E 298 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.7888 (t0) REVERT: E 316 GLN cc_start: 0.8705 (tp40) cc_final: 0.8273 (mm110) outliers start: 71 outliers final: 61 residues processed: 557 average time/residue: 0.2337 time to fit residues: 199.5809 Evaluate side-chains 583 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 516 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 88 TRP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 355 GLN Chi-restraints excluded: chain B residue 373 HIS Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 305 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 118 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 137 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 99 optimal weight: 0.4980 chunk 89 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 ASN C 373 HIS D 42 HIS ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN ** E 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.115109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.099315 restraints weight = 31005.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.102632 restraints weight = 15753.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.104931 restraints weight = 9561.765| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14910 Z= 0.215 Angle : 0.757 11.526 20230 Z= 0.358 Chirality : 0.047 0.189 2230 Planarity : 0.005 0.056 2590 Dihedral : 9.043 171.729 2075 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.89 % Allowed : 29.77 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.20), residues: 1840 helix: 0.19 (0.20), residues: 750 sheet: 0.53 (0.29), residues: 325 loop : 0.35 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 342 HIS 0.008 0.001 HIS D 175 PHE 0.045 0.001 PHE A 354 TYR 0.028 0.002 TYR A 145 ARG 0.007 0.001 ARG B 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5133.07 seconds wall clock time: 94 minutes 40.85 seconds (5680.85 seconds total)