Starting phenix.real_space_refine on Fri Jun 13 09:46:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ord_17120/06_2025/8ord_17120.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ord_17120/06_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_17120/06_2025/8ord_17120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ord_17120/06_2025/8ord_17120.map" model { file = "/net/cci-nas-00/data/ceres_data/8ord_17120/06_2025/8ord_17120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ord_17120/06_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-5710/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: 11.58, per 1000 atoms: 0.79 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: 3.45 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: 2.31 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: 6.45 Time building geometry restraints manager: 4.08 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: 0.000 Normalize map: mean=0, sd=1: 178.300 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: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 39.480 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:3.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 223.130 ------------------------------------------------------------------------------- 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 : 0.011 0.880 14912 Z= 1.035 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 Details of bonding type rmsd hydrogen bonds : bond 0.17471 ( 698) hydrogen bonds : angle 7.18406 ( 1809) covalent geometry : bond 0.00475 (14910) covalent geometry : angle 0.92138 (20230) Misc. bond : bond 0.87282 ( 2) *********************** 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 : 2.333 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: 0.3525 time to fit residues: 303.2752 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 : 1.955 ------------------------------------------------------------------------------- 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 = 0.097910 restraints weight = 30996.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.101235 restraints weight = 15614.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.103496 restraints weight = 9471.443| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 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 14912 Z= 0.164 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 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 698) hydrogen bonds : angle 5.49885 ( 1809) covalent geometry : bond 0.00368 (14910) covalent geometry : angle 0.73197 (20230) Misc. bond : bond 0.00115 ( 2) *********************** 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 : 1.993 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: 0.8409 (m90) cc_final: 0.8065 (m90) REVERT: A 142 LEU cc_start: 0.9276 (mt) cc_final: 0.8844 (mt) REVERT: A 145 TYR cc_start: 0.8143 (m-80) cc_final: 0.7277 (m-10) REVERT: A 212 ARG cc_start: 0.8455 (ttp80) cc_final: 0.8247 (tmm-80) REVERT: A 354 PHE cc_start: 0.8632 (t80) cc_final: 0.8260 (t80) REVERT: B 80 ASN cc_start: 0.8738 (t0) cc_final: 0.8476 (t0) REVERT: B 84 MET cc_start: 0.8400 (tpp) cc_final: 0.7137 (tpp) REVERT: B 88 TRP cc_start: 0.9382 (m-90) cc_final: 0.8774 (m-90) REVERT: B 115 LYS cc_start: 0.8916 (mmtp) cc_final: 0.8693 (mmmt) REVERT: B 123 GLN cc_start: 0.9154 (tt0) cc_final: 0.8401 (tp40) REVERT: B 134 MET cc_start: 0.8796 (ppp) cc_final: 0.8530 (tmm) REVERT: B 179 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.6651 (ttm170) REVERT: B 208 ARG cc_start: 0.8453 (ttp80) cc_final: 0.8149 (ttm-80) REVERT: B 272 GLU cc_start: 0.7512 (tt0) cc_final: 0.7276 (tt0) REVERT: B 316 GLN cc_start: 0.9102 (tm-30) cc_final: 0.8853 (tm-30) REVERT: C 248 GLN cc_start: 0.8783 (tt0) cc_final: 0.8064 (mt0) REVERT: C 286 LYS cc_start: 0.8914 (ttmm) cc_final: 0.8618 (mtpp) REVERT: C 327 MET cc_start: 0.8257 (mmt) cc_final: 0.7980 (mmm) REVERT: C 339 TYR cc_start: 0.8601 (m-80) cc_final: 0.8309 (m-10) REVERT: D 123 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8394 (tt0) REVERT: D 215 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8724 (tttp) REVERT: E 23 PHE cc_start: 0.8169 (m-80) cc_final: 0.7824 (m-80) REVERT: E 134 MET cc_start: 0.7827 (pmm) cc_final: 0.7489 (pmm) REVERT: E 191 LEU cc_start: 0.9010 (tp) cc_final: 0.8804 (tp) REVERT: E 193 LYS cc_start: 0.8980 (ttmt) cc_final: 0.8743 (ttmm) REVERT: E 209 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8644 (mm-30) REVERT: E 228 GLU cc_start: 0.8660 (tp30) cc_final: 0.8307 (tp30) REVERT: E 258 ARG cc_start: 0.9157 (mtm-85) cc_final: 0.7996 (ttm110) REVERT: E 298 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7497 (t0) outliers start: 68 outliers final: 50 residues processed: 571 average time/residue: 0.3233 time to fit residues: 275.6996 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 : 2.496 ------------------------------------------------------------------------------- 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: 6.9990 chunk 95 optimal weight: 3.9990 chunk 105 optimal weight: 0.0020 chunk 179 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 173 optimal weight: 0.3980 overall best weight: 0.2626 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.115427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.099422 restraints weight = 30885.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.102803 restraints weight = 15305.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.105089 restraints weight = 9187.112| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14912 Z= 0.120 Angle : 0.688 7.767 20230 Z= 0.330 Chirality : 0.046 0.171 2230 Planarity : 0.005 0.070 2590 Dihedral : 9.747 179.271 2078 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.41 % Allowed : 27.33 % Favored : 69.26 % 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: 0.08 (0.20), residues: 1840 helix: -0.09 (0.19), residues: 750 sheet: 0.37 (0.29), residues: 340 loop : 0.32 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 342 HIS 0.005 0.001 HIS C 89 PHE 0.011 0.001 PHE A 225 TYR 0.020 0.001 TYR A 168 ARG 0.007 0.001 ARG E 212 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 698) hydrogen bonds : angle 5.12030 ( 1809) covalent geometry : bond 0.00265 (14910) covalent geometry : angle 0.68767 (20230) Misc. bond : bond 0.00010 ( 2) *********************** 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 629 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 576 time to evaluate : 1.927 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: 0.7792 (tp-100) cc_final: 0.7297 (tp-100) REVERT: A 103 HIS cc_start: 0.8506 (m90) cc_final: 0.7930 (m90) REVERT: A 145 TYR cc_start: 0.8001 (m-80) cc_final: 0.7717 (m-10) REVERT: A 208 ARG cc_start: 0.8371 (mtm110) cc_final: 0.7881 (ttm-80) REVERT: A 212 ARG cc_start: 0.8464 (ttp80) cc_final: 0.8209 (tmm-80) REVERT: A 224 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.7948 (p0) REVERT: A 254 ASN cc_start: 0.9119 (p0) cc_final: 0.8706 (p0) REVERT: B 64 ARG cc_start: 0.9278 (ptt180) cc_final: 0.8743 (ptm160) REVERT: B 84 MET cc_start: 0.8410 (tpp) cc_final: 0.7143 (tpp) REVERT: B 88 TRP cc_start: 0.9288 (m-10) cc_final: 0.8737 (m-90) REVERT: B 123 GLN cc_start: 0.9308 (tt0) cc_final: 0.8866 (tp-100) REVERT: B 134 MET cc_start: 0.8904 (ppp) cc_final: 0.8573 (tmm) REVERT: B 169 GLU cc_start: 0.8845 (mp0) cc_final: 0.8396 (mm-30) REVERT: B 208 ARG cc_start: 0.8308 (ttp80) cc_final: 0.8102 (ttm-80) REVERT: B 223 LEU cc_start: 0.9091 (tt) cc_final: 0.8790 (tp) REVERT: B 256 ARG cc_start: 0.8564 (mtm180) cc_final: 0.8209 (mtm180) REVERT: B 272 GLU cc_start: 0.7431 (tt0) cc_final: 0.7075 (tt0) REVERT: B 316 GLN cc_start: 0.9143 (tm-30) cc_final: 0.8769 (tm-30) REVERT: B 331 MET cc_start: 0.8186 (mtt) cc_final: 0.7469 (mtt) REVERT: C 118 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8612 (mtm180) REVERT: C 125 MET cc_start: 0.9205 (mmp) cc_final: 0.8980 (mmp) REVERT: C 248 GLN cc_start: 0.8755 (tt0) cc_final: 0.8131 (mt0) REVERT: C 254 ASN cc_start: 0.8840 (OUTLIER) cc_final: 0.8385 (p0) REVERT: C 286 LYS cc_start: 0.8923 (ttmm) cc_final: 0.8589 (mtpp) REVERT: C 327 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7833 (mmm) REVERT: C 339 TYR cc_start: 0.8578 (m-80) cc_final: 0.8309 (m-10) REVERT: D 30 ARG cc_start: 0.7474 (mmm-85) cc_final: 0.6964 (mtp-110) REVERT: D 80 ASN cc_start: 0.8390 (t0) cc_final: 0.8143 (t0) REVERT: D 118 ARG cc_start: 0.8683 (ptt-90) cc_final: 0.8160 (ptt-90) REVERT: D 254 ASN cc_start: 0.9458 (p0) cc_final: 0.8916 (p0) REVERT: E 46 MET cc_start: 0.7602 (tpp) cc_final: 0.7392 (tpp) REVERT: E 191 LEU cc_start: 0.8977 (tp) cc_final: 0.8777 (tp) REVERT: E 193 LYS cc_start: 0.8939 (ttmt) cc_final: 0.8674 (ttmm) REVERT: E 212 ARG cc_start: 0.8658 (ttp80) cc_final: 0.8374 (ttp80) REVERT: E 228 GLU cc_start: 0.8738 (tp30) cc_final: 0.8296 (tp30) REVERT: E 258 ARG cc_start: 0.9053 (mtm-85) cc_final: 0.7885 (ttm110) outliers start: 53 outliers final: 37 residues processed: 597 average time/residue: 0.2782 time to fit residues: 253.0067 Evaluate side-chains 559 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 518 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 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 329 ILE 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 108 THR 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 348 LEU Chi-restraints excluded: chain B residue 353 THR 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 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 327 MET Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 117 ASN 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 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: 4.9990 chunk 58 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 13 optimal weight: 0.0770 chunk 168 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 149 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 143 optimal weight: 0.0870 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 HIS ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.112979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.097399 restraints weight = 31184.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.100640 restraints weight = 15817.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.102829 restraints weight = 9578.983| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14912 Z= 0.150 Angle : 0.686 7.900 20230 Z= 0.329 Chirality : 0.046 0.149 2230 Planarity : 0.005 0.060 2590 Dihedral : 9.502 173.564 2078 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 5.02 % Allowed : 26.69 % Favored : 68.30 % 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: 0.20 (0.20), residues: 1840 helix: 0.02 (0.20), residues: 750 sheet: 0.56 (0.30), residues: 325 loop : 0.29 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 342 HIS 0.010 0.001 HIS B 373 PHE 0.029 0.001 PHE A 225 TYR 0.021 0.001 TYR A 168 ARG 0.007 0.001 ARG E 212 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 698) hydrogen bonds : angle 5.01872 ( 1809) covalent geometry : bond 0.00345 (14910) covalent geometry : angle 0.68590 (20230) Misc. bond : bond 0.00055 ( 2) *********************** 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 618 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 540 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: A 43 GLN cc_start: 0.7861 (tp-100) cc_final: 0.7436 (tp-100) REVERT: A 103 HIS cc_start: 0.8466 (m90) cc_final: 0.7972 (m90) REVERT: A 145 TYR cc_start: 0.8090 (m-80) cc_final: 0.7678 (m-10) REVERT: A 212 ARG cc_start: 0.8495 (ttp80) cc_final: 0.8192 (tmm-80) REVERT: B 84 MET cc_start: 0.8606 (tpp) cc_final: 0.7316 (tpp) REVERT: B 88 TRP cc_start: 0.9339 (OUTLIER) cc_final: 0.8761 (m-90) REVERT: B 113 ASN cc_start: 0.9298 (t0) cc_final: 0.8952 (t0) REVERT: B 123 GLN cc_start: 0.9286 (tt0) cc_final: 0.8779 (tp-100) REVERT: B 169 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8268 (mm-30) REVERT: B 179 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.6588 (ttm170) REVERT: B 208 ARG cc_start: 0.8340 (ttp80) cc_final: 0.8125 (ttm-80) REVERT: B 223 LEU cc_start: 0.8991 (tt) cc_final: 0.8745 (tp) REVERT: B 256 ARG cc_start: 0.8591 (mtm180) cc_final: 0.8252 (mtm180) REVERT: B 272 GLU cc_start: 0.7540 (tt0) cc_final: 0.7173 (tt0) REVERT: B 281 TYR cc_start: 0.8887 (t80) cc_final: 0.8350 (t80) REVERT: B 316 GLN cc_start: 0.9139 (tm-30) cc_final: 0.8604 (tm-30) REVERT: B 358 TRP cc_start: 0.8066 (m-90) cc_final: 0.7548 (m-90) REVERT: C 12 CYS cc_start: 0.8713 (t) cc_final: 0.8277 (t) REVERT: C 61 GLN cc_start: 0.8323 (tp-100) cc_final: 0.8066 (tp40) REVERT: C 118 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8610 (mtp180) REVERT: C 171 TYR cc_start: 0.8508 (m-10) cc_final: 0.8290 (m-10) REVERT: C 248 GLN cc_start: 0.8769 (tt0) cc_final: 0.8141 (mt0) REVERT: C 254 ASN cc_start: 0.8885 (OUTLIER) cc_final: 0.8327 (p0) REVERT: C 286 LYS cc_start: 0.8955 (ttmm) cc_final: 0.8616 (mtpp) REVERT: C 288 ASP cc_start: 0.8088 (m-30) cc_final: 0.7819 (m-30) REVERT: C 327 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7854 (mmm) REVERT: D 30 ARG cc_start: 0.7502 (mmm-85) cc_final: 0.6985 (mtp-110) REVERT: D 80 ASN cc_start: 0.8493 (t0) cc_final: 0.8208 (t0) REVERT: D 118 ARG cc_start: 0.8731 (ptt-90) cc_final: 0.8224 (ptt-90) REVERT: D 225 PHE cc_start: 0.8128 (t80) cc_final: 0.7790 (t80) REVERT: D 254 ASN cc_start: 0.9403 (p0) cc_final: 0.8873 (p0) REVERT: D 316 GLN cc_start: 0.8386 (tm-30) cc_final: 0.8038 (tm-30) REVERT: D 351 LEU cc_start: 0.9029 (mm) cc_final: 0.8770 (mp) REVERT: E 30 ARG cc_start: 0.8361 (mmp80) cc_final: 0.7976 (mmm160) REVERT: E 126 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.7993 (m-10) REVERT: E 191 LEU cc_start: 0.9047 (tp) cc_final: 0.8731 (tt) REVERT: E 193 LYS cc_start: 0.8962 (ttmt) cc_final: 0.8688 (ttmm) REVERT: E 228 GLU cc_start: 0.8753 (tp30) cc_final: 0.8365 (tp30) REVERT: E 298 ASN cc_start: 0.8156 (t0) cc_final: 0.7734 (t0) outliers start: 78 outliers final: 53 residues processed: 567 average time/residue: 0.3079 time to fit residues: 270.5997 Evaluate side-chains 580 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 520 time to evaluate : 1.778 ------------------------------------------------------------------------------- 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 262 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain B residue 11 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 186 ASP Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 294 ASP 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 89 HIS 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 201 SER Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 327 MET Chi-restraints excluded: chain C residue 362 ASP 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 143 SER Chi-restraints excluded: chain D residue 153 ILE 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 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 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: 0.9990 chunk 182 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 141 optimal weight: 0.2980 chunk 132 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN 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 227 ASN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.113668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.098086 restraints weight = 31342.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.101356 restraints weight = 15836.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.103602 restraints weight = 9586.218| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14912 Z= 0.131 Angle : 0.680 9.205 20230 Z= 0.324 Chirality : 0.046 0.179 2230 Planarity : 0.005 0.060 2590 Dihedral : 9.317 164.876 2078 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 5.34 % Allowed : 26.95 % 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: 0.26 (0.20), residues: 1840 helix: 0.07 (0.20), residues: 750 sheet: 0.57 (0.29), residues: 325 loop : 0.33 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 342 HIS 0.006 0.001 HIS B 373 PHE 0.016 0.001 PHE A 225 TYR 0.021 0.001 TYR A 168 ARG 0.005 0.000 ARG A 30 Details of bonding type rmsd hydrogen bonds : bond 0.03296 ( 698) hydrogen bonds : angle 4.97107 ( 1809) covalent geometry : bond 0.00304 (14910) covalent geometry : angle 0.68018 (20230) Misc. bond : bond 0.00049 ( 2) *********************** 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 636 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 553 time to evaluate : 1.679 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: 0.7887 (tp-100) cc_final: 0.7427 (tp-100) REVERT: A 70 LYS cc_start: 0.8718 (mmmm) cc_final: 0.8434 (mmmm) REVERT: A 103 HIS cc_start: 0.8439 (m90) cc_final: 0.8009 (m90) REVERT: A 118 ARG cc_start: 0.8720 (ptt180) cc_final: 0.8362 (ptt180) REVERT: A 208 ARG cc_start: 0.8391 (mtm110) cc_final: 0.7924 (ttm-80) REVERT: A 212 ARG cc_start: 0.8494 (ttp80) cc_final: 0.8199 (tmm-80) REVERT: A 224 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8158 (p0) REVERT: A 298 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.6768 (t0) REVERT: A 327 MET cc_start: 0.8475 (mmp) cc_final: 0.8070 (mmt) REVERT: B 84 MET cc_start: 0.8645 (tpp) cc_final: 0.7384 (tpp) REVERT: B 88 TRP cc_start: 0.9328 (OUTLIER) cc_final: 0.8765 (m-90) REVERT: B 113 ASN cc_start: 0.9314 (t0) cc_final: 0.8978 (t0) REVERT: B 119 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8572 (mt-10) REVERT: B 123 GLN cc_start: 0.9258 (tt0) cc_final: 0.8915 (tp40) REVERT: B 169 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8222 (mm-30) REVERT: B 179 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.6563 (ttm170) REVERT: B 208 ARG cc_start: 0.8309 (ttp80) cc_final: 0.8104 (ttm-80) REVERT: B 223 LEU cc_start: 0.8959 (tt) cc_final: 0.8726 (tp) REVERT: B 272 GLU cc_start: 0.7505 (tt0) cc_final: 0.7170 (tt0) REVERT: B 281 TYR cc_start: 0.8861 (t80) cc_final: 0.8354 (t80) REVERT: B 316 GLN cc_start: 0.9007 (tm-30) cc_final: 0.8490 (tm-30) REVERT: B 357 MET cc_start: 0.8559 (mmm) cc_final: 0.8286 (mtp) REVERT: C 12 CYS cc_start: 0.8673 (t) cc_final: 0.8083 (t) REVERT: C 14 ASN cc_start: 0.7685 (m110) cc_final: 0.6889 (m-40) REVERT: C 118 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8336 (mtp-110) REVERT: C 123 GLN cc_start: 0.8627 (tt0) cc_final: 0.8251 (tm-30) REVERT: C 248 GLN cc_start: 0.8751 (tt0) cc_final: 0.8099 (mt0) REVERT: C 254 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8277 (p0) REVERT: C 288 ASP cc_start: 0.8137 (m-30) cc_final: 0.7820 (m-30) REVERT: C 298 ASN cc_start: 0.8411 (m-40) cc_final: 0.7503 (t0) REVERT: C 316 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8518 (tm-30) REVERT: C 327 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7782 (mmm) REVERT: C 339 TYR cc_start: 0.8572 (m-80) cc_final: 0.8152 (m-80) REVERT: C 342 TRP cc_start: 0.8009 (t60) cc_final: 0.7060 (t60) REVERT: D 80 ASN cc_start: 0.8473 (t0) cc_final: 0.8156 (t0) REVERT: D 115 LYS cc_start: 0.8258 (mmtt) cc_final: 0.7599 (ptpp) REVERT: D 118 ARG cc_start: 0.8708 (ptt-90) cc_final: 0.8066 (ptt-90) REVERT: D 225 PHE cc_start: 0.8125 (t80) cc_final: 0.7878 (t80) REVERT: D 254 ASN cc_start: 0.9400 (p0) cc_final: 0.8829 (p0) REVERT: D 316 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7930 (tm-30) REVERT: D 348 LEU cc_start: 0.8511 (tp) cc_final: 0.8222 (tp) REVERT: D 351 LEU cc_start: 0.9064 (mm) cc_final: 0.8827 (mp) REVERT: E 30 ARG cc_start: 0.8356 (mmp80) cc_final: 0.8030 (mmm160) REVERT: E 126 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.7943 (m-10) REVERT: E 151 THR cc_start: 0.8818 (p) cc_final: 0.8570 (t) REVERT: E 159 ASP cc_start: 0.8552 (t0) cc_final: 0.8316 (t0) REVERT: E 193 LYS cc_start: 0.8961 (ttmt) cc_final: 0.8684 (ttmm) REVERT: E 228 GLU cc_start: 0.8718 (tp30) cc_final: 0.8391 (tp30) REVERT: E 290 ASP cc_start: 0.6970 (p0) cc_final: 0.6439 (p0) REVERT: E 298 ASN cc_start: 0.8169 (t0) cc_final: 0.7688 (t0) outliers start: 83 outliers final: 61 residues processed: 584 average time/residue: 0.2328 time to fit residues: 206.7247 Evaluate side-chains 589 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 519 time to evaluate : 1.648 ------------------------------------------------------------------------------- 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 224 ASP Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 298 ASN 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 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 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 262 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 353 THR 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 161 VAL 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 C residue 362 ASP 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 255 GLU 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 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 299 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: 0.7980 chunk 2 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 105 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 161 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 254 ASN D 355 GLN E 14 ASN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 ASN ** 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 = 0.3404 r_free = 0.3404 target = 0.113436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.097788 restraints weight = 31151.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.101047 restraints weight = 15662.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.103252 restraints weight = 9476.806| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14912 Z= 0.134 Angle : 0.683 8.570 20230 Z= 0.325 Chirality : 0.046 0.157 2230 Planarity : 0.005 0.058 2590 Dihedral : 9.075 156.024 2078 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 5.53 % Allowed : 27.07 % Favored : 67.40 % 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: 0.31 (0.20), residues: 1840 helix: 0.12 (0.20), residues: 750 sheet: 0.59 (0.29), residues: 325 loop : 0.37 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 342 HIS 0.006 0.001 HIS B 373 PHE 0.014 0.001 PHE A 225 TYR 0.023 0.001 TYR A 145 ARG 0.006 0.001 ARG B 292 Details of bonding type rmsd hydrogen bonds : bond 0.03240 ( 698) hydrogen bonds : angle 4.93345 ( 1809) covalent geometry : bond 0.00311 (14910) covalent geometry : angle 0.68333 (20230) Misc. bond : bond 0.00047 ( 2) *********************** 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 630 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 544 time to evaluate : 1.553 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: 0.8050 (tp-100) cc_final: 0.7723 (tp-100) REVERT: A 70 LYS cc_start: 0.8725 (mmmm) cc_final: 0.8267 (mmmm) REVERT: A 103 HIS cc_start: 0.8475 (m90) cc_final: 0.8035 (m90) REVERT: A 118 ARG cc_start: 0.8768 (ptt180) cc_final: 0.8445 (ptt180) REVERT: A 212 ARG cc_start: 0.8450 (ttp80) cc_final: 0.8127 (tmm-80) REVERT: B 113 ASN cc_start: 0.9305 (t0) cc_final: 0.8925 (t0) REVERT: B 115 LYS cc_start: 0.9011 (mmmt) cc_final: 0.8721 (mmmt) REVERT: B 119 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8592 (mt-10) REVERT: B 123 GLN cc_start: 0.9265 (tt0) cc_final: 0.8838 (tp40) REVERT: B 169 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8223 (mm-30) REVERT: B 179 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.6549 (ttm170) REVERT: B 208 ARG cc_start: 0.8309 (ttp80) cc_final: 0.8093 (ttm-80) REVERT: B 272 GLU cc_start: 0.7476 (tt0) cc_final: 0.7149 (tt0) REVERT: B 281 TYR cc_start: 0.8841 (t80) cc_final: 0.8369 (t80) REVERT: B 307 MET cc_start: 0.8552 (mtp) cc_final: 0.8316 (mtp) REVERT: B 316 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8505 (tm-30) REVERT: B 357 MET cc_start: 0.8620 (mmm) cc_final: 0.8259 (mtp) REVERT: B 363 GLU cc_start: 0.8804 (tp30) cc_final: 0.8598 (tp30) REVERT: C 12 CYS cc_start: 0.8716 (t) cc_final: 0.8131 (t) REVERT: C 14 ASN cc_start: 0.7650 (m110) cc_final: 0.6847 (m-40) REVERT: C 118 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8348 (mtp-110) REVERT: C 123 GLN cc_start: 0.8619 (tt0) cc_final: 0.8300 (tm-30) REVERT: C 248 GLN cc_start: 0.8736 (tt0) cc_final: 0.8104 (mt0) REVERT: C 254 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8276 (p0) REVERT: C 288 ASP cc_start: 0.8206 (m-30) cc_final: 0.7909 (m-30) REVERT: C 298 ASN cc_start: 0.8428 (m-40) cc_final: 0.7573 (t0) REVERT: C 316 GLN cc_start: 0.8886 (tm-30) cc_final: 0.8424 (tm-30) REVERT: C 327 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7655 (mmm) REVERT: C 342 TRP cc_start: 0.7977 (t60) cc_final: 0.7172 (t60) REVERT: D 80 ASN cc_start: 0.8433 (t0) cc_final: 0.8089 (t0) REVERT: D 115 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7382 (ptpp) REVERT: D 118 ARG cc_start: 0.8743 (ptt-90) cc_final: 0.8182 (ptt-90) REVERT: D 225 PHE cc_start: 0.8309 (t80) cc_final: 0.7975 (t80) REVERT: D 254 ASN cc_start: 0.9403 (p0) cc_final: 0.8801 (p0) REVERT: D 316 GLN cc_start: 0.8263 (tm-30) cc_final: 0.8014 (tm-30) REVERT: D 348 LEU cc_start: 0.8476 (tp) cc_final: 0.8158 (tp) REVERT: D 351 LEU cc_start: 0.9063 (mm) cc_final: 0.8811 (mp) REVERT: E 30 ARG cc_start: 0.8413 (mmp80) cc_final: 0.8145 (mmp-170) REVERT: E 126 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7892 (m-10) REVERT: E 151 THR cc_start: 0.8855 (p) cc_final: 0.8592 (t) REVERT: E 159 ASP cc_start: 0.8581 (t0) cc_final: 0.8352 (t0) REVERT: E 193 LYS cc_start: 0.8970 (ttmt) cc_final: 0.8709 (ttmm) REVERT: E 228 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8424 (tp30) REVERT: E 298 ASN cc_start: 0.8210 (t0) cc_final: 0.7731 (t0) outliers start: 86 outliers final: 67 residues processed: 575 average time/residue: 0.2326 time to fit residues: 203.3452 Evaluate side-chains 587 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 513 time to evaluate : 1.573 ------------------------------------------------------------------------------- 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 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 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 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 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 89 HIS 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 161 VAL 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 C residue 362 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 188 THR Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 276 ILE 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 69 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 228 GLU Chi-restraints excluded: chain E residue 299 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: 2.9990 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN B 90 HIS ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.106242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.090838 restraints weight = 32766.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.093893 restraints weight = 16556.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096031 restraints weight = 10104.808| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 14912 Z= 0.302 Angle : 0.803 10.433 20230 Z= 0.391 Chirality : 0.050 0.177 2230 Planarity : 0.005 0.057 2590 Dihedral : 9.261 158.794 2078 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 5.66 % Allowed : 27.85 % Favored : 66.50 % 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: 0.07 (0.20), residues: 1840 helix: -0.00 (0.19), residues: 755 sheet: 0.25 (0.30), residues: 335 loop : 0.26 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 342 HIS 0.012 0.002 HIS B 373 PHE 0.021 0.002 PHE A 225 TYR 0.030 0.002 TYR C 168 ARG 0.006 0.001 ARG A 30 Details of bonding type rmsd hydrogen bonds : bond 0.03928 ( 698) hydrogen bonds : angle 5.29465 ( 1809) covalent geometry : bond 0.00674 (14910) covalent geometry : angle 0.80305 (20230) Misc. bond : bond 0.00071 ( 2) *********************** 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 588 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 500 time to evaluate : 1.683 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: 0.8205 (tp-100) cc_final: 0.7817 (tp-100) REVERT: A 70 LYS cc_start: 0.8814 (mmmm) cc_final: 0.8441 (mmmm) REVERT: A 103 HIS cc_start: 0.8528 (m90) cc_final: 0.8021 (m90) REVERT: A 118 ARG cc_start: 0.8817 (ptt180) cc_final: 0.8443 (ptt180) REVERT: A 224 ASP cc_start: 0.8790 (OUTLIER) cc_final: 0.8347 (p0) REVERT: A 254 ASN cc_start: 0.9188 (p0) cc_final: 0.8819 (p0) REVERT: B 58 ASP cc_start: 0.8887 (t0) cc_final: 0.8515 (t0) REVERT: B 88 TRP cc_start: 0.9405 (m-10) cc_final: 0.8836 (m-90) REVERT: B 113 ASN cc_start: 0.9420 (t0) cc_final: 0.8217 (t0) REVERT: B 117 ASN cc_start: 0.8967 (t0) cc_final: 0.8706 (t0) REVERT: B 119 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8656 (mt-10) REVERT: B 123 GLN cc_start: 0.9334 (tt0) cc_final: 0.8742 (tp-100) REVERT: B 169 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8373 (mm-30) REVERT: B 179 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.6569 (ttm170) REVERT: B 208 ARG cc_start: 0.8532 (ttp80) cc_final: 0.8151 (ttm-80) REVERT: B 223 LEU cc_start: 0.9046 (tt) cc_final: 0.8762 (tp) REVERT: B 281 TYR cc_start: 0.8961 (t80) cc_final: 0.8454 (t80) REVERT: B 357 MET cc_start: 0.8815 (mmm) cc_final: 0.7955 (mmm) REVERT: C 27 ASP cc_start: 0.8463 (t0) cc_final: 0.8218 (t0) REVERT: C 118 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8467 (mtp180) REVERT: C 123 GLN cc_start: 0.8774 (tt0) cc_final: 0.8376 (tm-30) REVERT: C 229 MET cc_start: 0.8689 (mmt) cc_final: 0.8406 (mmm) REVERT: C 248 GLN cc_start: 0.8782 (tt0) cc_final: 0.8170 (mt0) REVERT: C 254 ASN cc_start: 0.8858 (OUTLIER) cc_final: 0.8422 (p0) REVERT: C 288 ASP cc_start: 0.8287 (m-30) cc_final: 0.8049 (m-30) REVERT: C 358 TRP cc_start: 0.8751 (m100) cc_final: 0.8362 (m100) REVERT: D 80 ASN cc_start: 0.8528 (t0) cc_final: 0.8152 (t0) REVERT: D 225 PHE cc_start: 0.8442 (t80) cc_final: 0.8095 (t80) REVERT: D 316 GLN cc_start: 0.8445 (tm-30) cc_final: 0.8140 (tm-30) REVERT: E 30 ARG cc_start: 0.8527 (mmp80) cc_final: 0.8197 (mmp-170) REVERT: E 43 GLN cc_start: 0.8201 (tp-100) cc_final: 0.7774 (tp-100) REVERT: E 122 THR cc_start: 0.8824 (m) cc_final: 0.8513 (t) REVERT: E 126 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7969 (m-10) REVERT: E 193 LYS cc_start: 0.9019 (ttmt) cc_final: 0.8761 (ttmm) REVERT: E 228 GLU cc_start: 0.8812 (tp30) cc_final: 0.8431 (tp30) REVERT: E 272 GLU cc_start: 0.5155 (pt0) cc_final: 0.3961 (tt0) REVERT: E 278 GLU cc_start: 0.8409 (tm-30) cc_final: 0.7233 (tm-30) outliers start: 88 outliers final: 68 residues processed: 536 average time/residue: 0.2293 time to fit residues: 187.3518 Evaluate side-chains 555 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 481 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 262 THR 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 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 186 ASP Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 262 THR 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 94 ASN 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 141 VAL 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 254 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 372 VAL 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 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 36 ILE Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 80 ASN 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 243 GLU Chi-restraints excluded: chain E residue 269 ILE 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: 0.5980 chunk 91 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 149 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 HIS ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 GLN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 ASN ** 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 = 0.3363 r_free = 0.3363 target = 0.110190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.094834 restraints weight = 31525.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.097927 restraints weight = 15970.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.100094 restraints weight = 9769.652| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14912 Z= 0.163 Angle : 0.737 9.569 20230 Z= 0.353 Chirality : 0.047 0.181 2230 Planarity : 0.005 0.058 2590 Dihedral : 9.057 156.302 2075 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.95 % Allowed : 29.39 % Favored : 65.66 % 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: 0.13 (0.20), residues: 1840 helix: 0.02 (0.19), residues: 750 sheet: 0.46 (0.30), residues: 325 loop : 0.23 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP C 342 HIS 0.009 0.001 HIS B 373 PHE 0.016 0.001 PHE A 225 TYR 0.020 0.002 TYR C 168 ARG 0.006 0.001 ARG A 30 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 698) hydrogen bonds : angle 5.05990 ( 1809) covalent geometry : bond 0.00380 (14910) covalent geometry : angle 0.73724 (20230) Misc. bond : bond 0.00057 ( 2) *********************** 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 608 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 531 time to evaluate : 1.469 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: 0.8205 (tp-100) cc_final: 0.7829 (tp-100) REVERT: A 70 LYS cc_start: 0.8795 (mmmm) cc_final: 0.8428 (mmmm) REVERT: A 103 HIS cc_start: 0.8516 (m90) cc_final: 0.8043 (m90) REVERT: A 118 ARG cc_start: 0.8755 (ptt180) cc_final: 0.8382 (ptt180) REVERT: A 212 ARG cc_start: 0.8479 (ttp80) cc_final: 0.8200 (tmm-80) REVERT: A 254 ASN cc_start: 0.9210 (p0) cc_final: 0.8787 (p0) REVERT: A 278 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8451 (mp0) REVERT: B 58 ASP cc_start: 0.8822 (t0) cc_final: 0.8470 (t0) REVERT: B 88 TRP cc_start: 0.9319 (m-10) cc_final: 0.8838 (m-90) REVERT: B 90 HIS cc_start: 0.8945 (t70) cc_final: 0.8044 (t-90) REVERT: B 95 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8369 (mm-30) REVERT: B 113 ASN cc_start: 0.9361 (t0) cc_final: 0.8377 (t0) REVERT: B 115 LYS cc_start: 0.9075 (mmmt) cc_final: 0.8715 (mmmt) REVERT: B 119 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8614 (mt-10) REVERT: B 123 GLN cc_start: 0.9292 (tt0) cc_final: 0.8719 (tp-100) REVERT: B 149 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.6612 (mpp80) REVERT: B 169 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8237 (mm-30) REVERT: B 179 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.6623 (ttm170) REVERT: B 208 ARG cc_start: 0.8493 (ttp80) cc_final: 0.8154 (ttm-80) REVERT: B 223 LEU cc_start: 0.8980 (tt) cc_final: 0.8720 (tp) REVERT: B 281 TYR cc_start: 0.8903 (t80) cc_final: 0.8314 (t80) REVERT: B 357 MET cc_start: 0.8740 (mmm) cc_final: 0.7851 (mmm) REVERT: C 118 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8567 (mtp180) REVERT: C 123 GLN cc_start: 0.8680 (tt0) cc_final: 0.8370 (tm-30) REVERT: C 248 GLN cc_start: 0.8799 (tt0) cc_final: 0.8103 (mt0) REVERT: C 255 GLU cc_start: 0.8823 (pm20) cc_final: 0.8536 (pm20) REVERT: C 288 ASP cc_start: 0.8237 (m-30) cc_final: 0.7982 (m-30) REVERT: C 316 GLN cc_start: 0.8909 (tm-30) cc_final: 0.8445 (tm-30) REVERT: C 339 TYR cc_start: 0.8613 (m-80) cc_final: 0.8270 (m-10) REVERT: C 358 TRP cc_start: 0.8731 (m100) cc_final: 0.8364 (m100) REVERT: D 80 ASN cc_start: 0.8457 (t0) cc_final: 0.8098 (t0) REVERT: D 118 ARG cc_start: 0.8745 (ptt-90) cc_final: 0.8139 (ptt-90) REVERT: D 225 PHE cc_start: 0.8370 (t80) cc_final: 0.8099 (t80) REVERT: D 351 LEU cc_start: 0.9230 (mm) cc_final: 0.8954 (mp) REVERT: E 30 ARG cc_start: 0.8554 (mmp80) cc_final: 0.8076 (mmp-170) REVERT: E 43 GLN cc_start: 0.8217 (tp-100) cc_final: 0.7803 (tp-100) REVERT: E 122 THR cc_start: 0.8772 (m) cc_final: 0.8458 (t) REVERT: E 126 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.7948 (m-10) REVERT: E 193 LYS cc_start: 0.8988 (ttmt) cc_final: 0.8693 (ttmm) REVERT: E 228 GLU cc_start: 0.8842 (tp30) cc_final: 0.8456 (tp30) REVERT: E 278 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7104 (tm-30) outliers start: 77 outliers final: 65 residues processed: 558 average time/residue: 0.2407 time to fit residues: 205.1972 Evaluate side-chains 575 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 505 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU 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 224 ASP 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 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 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 66 ILE Chi-restraints excluded: chain C residue 83 ASP 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 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 362 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 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 161 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 69 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 188 THR Chi-restraints excluded: chain E residue 243 GLU 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: 0.6980 chunk 92 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 130 optimal weight: 0.0870 chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 128 optimal weight: 0.5980 chunk 164 optimal weight: 0.3980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN A 164 ASN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN D 42 HIS ** E 113 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.098546 restraints weight = 31013.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.101764 restraints weight = 15662.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.103975 restraints weight = 9508.457| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14912 Z= 0.132 Angle : 0.742 10.147 20230 Z= 0.354 Chirality : 0.046 0.195 2230 Planarity : 0.005 0.056 2590 Dihedral : 8.865 152.258 2075 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.99 % Allowed : 30.42 % Favored : 65.59 % 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: 0.19 (0.20), residues: 1840 helix: 0.05 (0.20), residues: 750 sheet: 0.49 (0.29), residues: 325 loop : 0.28 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 342 HIS 0.010 0.001 HIS B 373 PHE 0.013 0.001 PHE C 129 TYR 0.032 0.001 TYR A 145 ARG 0.007 0.000 ARG A 30 Details of bonding type rmsd hydrogen bonds : bond 0.03276 ( 698) hydrogen bonds : angle 4.99291 ( 1809) covalent geometry : bond 0.00311 (14910) covalent geometry : angle 0.74208 (20230) Misc. bond : bond 0.00037 ( 2) *********************** 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 588 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 526 time to evaluate : 1.538 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: 0.8200 (tp-100) cc_final: 0.7908 (tp-100) REVERT: A 51 GLN cc_start: 0.5358 (mp10) cc_final: 0.5063 (mp10) REVERT: A 70 LYS cc_start: 0.8751 (mmmm) cc_final: 0.8386 (mmmm) REVERT: A 84 MET cc_start: 0.8166 (tpt) cc_final: 0.7877 (tpt) REVERT: A 103 HIS cc_start: 0.8530 (m90) cc_final: 0.8050 (m90) REVERT: A 115 LYS cc_start: 0.8220 (mmtt) cc_final: 0.7922 (mmtt) REVERT: A 118 ARG cc_start: 0.8751 (ptt180) cc_final: 0.8409 (ptt180) REVERT: A 212 ARG cc_start: 0.8430 (ttp80) cc_final: 0.8160 (tmm-80) REVERT: A 278 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8447 (mp0) REVERT: B 58 ASP cc_start: 0.8777 (t0) cc_final: 0.8409 (t0) REVERT: B 83 ASP cc_start: 0.8661 (m-30) cc_final: 0.8374 (p0) REVERT: B 88 TRP cc_start: 0.9261 (OUTLIER) cc_final: 0.8832 (m-90) REVERT: B 90 HIS cc_start: 0.8924 (t70) cc_final: 0.7782 (t-90) REVERT: B 95 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8223 (mm-30) REVERT: B 115 LYS cc_start: 0.9011 (mmmt) cc_final: 0.7806 (mmtm) REVERT: B 119 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8501 (mt-10) REVERT: B 123 GLN cc_start: 0.9308 (tt0) cc_final: 0.8866 (tp40) REVERT: B 149 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.6683 (mpp80) REVERT: B 169 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8200 (mm-30) REVERT: B 208 ARG cc_start: 0.8390 (ttp80) cc_final: 0.8112 (ttm-80) REVERT: B 223 LEU cc_start: 0.8962 (tt) cc_final: 0.8711 (tp) REVERT: B 281 TYR cc_start: 0.8844 (t80) cc_final: 0.8344 (t80) REVERT: B 357 MET cc_start: 0.8733 (mmm) cc_final: 0.7778 (mmm) REVERT: C 118 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8463 (mtp180) REVERT: C 123 GLN cc_start: 0.8596 (tt0) cc_final: 0.8326 (tm-30) REVERT: C 168 TYR cc_start: 0.8457 (t80) cc_final: 0.8086 (t80) REVERT: C 169 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8100 (mm-30) REVERT: C 248 GLN cc_start: 0.8756 (tt0) cc_final: 0.8090 (mt0) REVERT: C 288 ASP cc_start: 0.8227 (m-30) cc_final: 0.7964 (m-30) REVERT: C 339 TYR cc_start: 0.8648 (m-80) cc_final: 0.8283 (m-10) REVERT: C 358 TRP cc_start: 0.8689 (m100) cc_final: 0.8333 (m100) REVERT: D 80 ASN cc_start: 0.8411 (t0) cc_final: 0.8044 (t0) REVERT: D 115 LYS cc_start: 0.8359 (mmtm) cc_final: 0.8152 (tppt) REVERT: D 118 ARG cc_start: 0.8520 (ptt-90) cc_final: 0.7953 (ptt-90) REVERT: D 316 GLN cc_start: 0.8045 (tm-30) cc_final: 0.7751 (tm-30) REVERT: D 351 LEU cc_start: 0.9159 (mm) cc_final: 0.8885 (mp) REVERT: E 30 ARG cc_start: 0.8511 (mmp80) cc_final: 0.8050 (mmp-170) REVERT: E 43 GLN cc_start: 0.8263 (tp-100) cc_final: 0.7842 (tp-100) REVERT: E 113 ASN cc_start: 0.8660 (t160) cc_final: 0.8343 (t0) REVERT: E 122 THR cc_start: 0.8758 (m) cc_final: 0.8430 (t) REVERT: E 126 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7865 (m-10) REVERT: E 191 LEU cc_start: 0.8999 (tp) cc_final: 0.8695 (tt) REVERT: E 193 LYS cc_start: 0.8960 (ttmt) cc_final: 0.8683 (ttmm) REVERT: E 228 GLU cc_start: 0.8826 (tp30) cc_final: 0.8437 (tp30) REVERT: E 272 GLU cc_start: 0.5013 (pt0) cc_final: 0.3863 (tt0) REVERT: E 278 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7127 (tm-30) REVERT: E 290 ASP cc_start: 0.7177 (p0) cc_final: 0.6883 (p0) outliers start: 62 outliers final: 47 residues processed: 546 average time/residue: 0.2281 time to fit residues: 189.1146 Evaluate side-chains 569 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 517 time to evaluate : 1.601 ------------------------------------------------------------------------------- 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 262 THR 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 88 TRP 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 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 66 ILE Chi-restraints excluded: chain C residue 83 ASP 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 161 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 32 VAL 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 187 LEU Chi-restraints excluded: chain D residue 276 ILE 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 153 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 299 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: 1.9990 chunk 116 optimal weight: 0.0030 chunk 59 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 173 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN A 373 HIS ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 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 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.112862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.097349 restraints weight = 31339.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.100547 restraints weight = 15865.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.102771 restraints weight = 9644.172| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14912 Z= 0.146 Angle : 0.761 10.706 20230 Z= 0.364 Chirality : 0.047 0.180 2230 Planarity : 0.005 0.056 2590 Dihedral : 8.812 149.903 2075 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.79 % Allowed : 31.00 % Favored : 65.21 % 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: 0.13 (0.20), residues: 1840 helix: 0.05 (0.20), residues: 750 sheet: 0.47 (0.29), residues: 325 loop : 0.18 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 342 HIS 0.010 0.001 HIS B 373 PHE 0.011 0.001 PHE C 129 TYR 0.014 0.001 TYR A 168 ARG 0.007 0.001 ARG A 30 Details of bonding type rmsd hydrogen bonds : bond 0.03303 ( 698) hydrogen bonds : angle 4.99324 ( 1809) covalent geometry : bond 0.00342 (14910) covalent geometry : angle 0.76124 (20230) Misc. bond : bond 0.00036 ( 2) ********************** 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 579 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 520 time to evaluate : 1.628 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: A 43 GLN cc_start: 0.8175 (tp-100) cc_final: 0.7974 (tp-100) REVERT: A 51 GLN cc_start: 0.5339 (mp10) cc_final: 0.5059 (mp10) REVERT: A 70 LYS cc_start: 0.8759 (mmmm) cc_final: 0.8399 (mmmm) REVERT: A 84 MET cc_start: 0.8149 (tpt) cc_final: 0.7882 (tpt) REVERT: A 103 HIS cc_start: 0.8485 (m90) cc_final: 0.8030 (m90) REVERT: A 118 ARG cc_start: 0.8666 (ptt180) cc_final: 0.8381 (ptt180) REVERT: A 212 ARG cc_start: 0.8488 (ttp80) cc_final: 0.8225 (tmm-80) REVERT: A 278 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8448 (mp0) REVERT: B 83 ASP cc_start: 0.8610 (m-30) cc_final: 0.8373 (p0) REVERT: B 90 HIS cc_start: 0.8843 (t70) cc_final: 0.7810 (t-90) REVERT: B 95 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8157 (mm-30) REVERT: B 115 LYS cc_start: 0.8783 (mmmt) cc_final: 0.8343 (mmmt) REVERT: B 119 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8688 (mt-10) REVERT: B 123 GLN cc_start: 0.9265 (tt0) cc_final: 0.8575 (tp-100) REVERT: B 149 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.6684 (mpp80) REVERT: B 169 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8063 (mm-30) REVERT: B 223 LEU cc_start: 0.8975 (tt) cc_final: 0.8730 (tp) REVERT: B 281 TYR cc_start: 0.8854 (t80) cc_final: 0.8348 (t80) REVERT: B 357 MET cc_start: 0.8709 (mmm) cc_final: 0.7816 (mmm) REVERT: C 113 ASN cc_start: 0.8985 (t0) cc_final: 0.8411 (t0) REVERT: C 118 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8504 (mtp180) REVERT: C 123 GLN cc_start: 0.8605 (tt0) cc_final: 0.8362 (tm-30) REVERT: C 197 GLU cc_start: 0.7536 (tp30) cc_final: 0.7265 (tp30) REVERT: C 248 GLN cc_start: 0.8772 (tt0) cc_final: 0.8099 (mt0) REVERT: C 288 ASP cc_start: 0.8193 (m-30) cc_final: 0.7956 (m-30) REVERT: C 298 ASN cc_start: 0.8339 (m-40) cc_final: 0.7331 (t0) REVERT: C 339 TYR cc_start: 0.8621 (m-80) cc_final: 0.8252 (m-10) REVERT: C 342 TRP cc_start: 0.8236 (t60) cc_final: 0.6349 (t60) REVERT: C 358 TRP cc_start: 0.8738 (m100) cc_final: 0.8392 (m100) REVERT: D 80 ASN cc_start: 0.8421 (t0) cc_final: 0.8083 (t0) REVERT: D 118 ARG cc_start: 0.8566 (ptt-90) cc_final: 0.8128 (ptt-90) REVERT: D 258 ARG cc_start: 0.8711 (mtp85) cc_final: 0.8503 (mtp85) REVERT: D 316 GLN cc_start: 0.8114 (tm-30) cc_final: 0.7661 (tm-30) REVERT: D 351 LEU cc_start: 0.9165 (mm) cc_final: 0.8862 (mp) REVERT: E 30 ARG cc_start: 0.8562 (mmp80) cc_final: 0.8110 (mmp-170) REVERT: E 43 GLN cc_start: 0.8228 (tp-100) cc_final: 0.7837 (tp-100) REVERT: E 113 ASN cc_start: 0.8693 (t160) cc_final: 0.8386 (t0) REVERT: E 122 THR cc_start: 0.8789 (m) cc_final: 0.8451 (t) REVERT: E 126 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7867 (m-10) REVERT: E 191 LEU cc_start: 0.9011 (tp) cc_final: 0.8714 (tt) REVERT: E 193 LYS cc_start: 0.8978 (ttmt) cc_final: 0.8705 (ttmm) REVERT: E 228 GLU cc_start: 0.8762 (tp30) cc_final: 0.8426 (tp30) REVERT: E 272 GLU cc_start: 0.5094 (pt0) cc_final: 0.3929 (tt0) REVERT: E 278 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7157 (tm-30) REVERT: E 316 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8183 (mm110) outliers start: 59 outliers final: 53 residues processed: 544 average time/residue: 0.2323 time to fit residues: 191.7437 Evaluate side-chains 563 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 506 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU 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 227 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 355 GLN 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 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 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 66 ILE Chi-restraints excluded: chain C residue 83 ASP 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 161 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 143 SER 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 276 ILE Chi-restraints excluded: chain E residue 18 LEU 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 299 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: 0.9980 chunk 130 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 168 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 99 optimal weight: 0.3980 chunk 89 optimal weight: 0.7980 chunk 177 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.112802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.097115 restraints weight = 31235.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.100366 restraints weight = 15660.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.102592 restraints weight = 9466.669| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.247 14912 Z= 0.232 Angle : 0.953 59.199 20230 Z= 0.500 Chirality : 0.046 0.168 2230 Planarity : 0.005 0.056 2590 Dihedral : 8.808 149.885 2075 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.92 % Allowed : 31.25 % Favored : 64.82 % Cbeta Deviations : 0.06 % 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: 0.14 (0.20), residues: 1840 helix: 0.06 (0.20), residues: 750 sheet: 0.47 (0.29), residues: 325 loop : 0.20 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 342 HIS 0.038 0.002 HIS D 373 PHE 0.011 0.001 PHE E 257 TYR 0.016 0.001 TYR C 168 ARG 0.023 0.001 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.03421 ( 698) hydrogen bonds : angle 4.99435 ( 1809) covalent geometry : bond 0.00531 (14910) covalent geometry : angle 0.95309 (20230) Misc. bond : bond 0.00037 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6054.92 seconds wall clock time: 108 minutes 45.59 seconds (6525.59 seconds total)