Starting phenix.real_space_refine on Sat Aug 23 21:43:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ord_17120/08_2025/8ord_17120.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ord_17120/08_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_17120/08_2025/8ord_17120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ord_17120/08_2025/8ord_17120.map" model { file = "/net/cci-nas-00/data/ceres_data/8ord_17120/08_2025/8ord_17120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ord_17120/08_2025/8ord_17120.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.83, per 1000 atoms: 0.19 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: 0.91 Conformation dependent library (CDL) restraints added in 506.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.41 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: 2.07 Time building geometry restraints manager: 1.22 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: 0.01 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: 8.750 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.340 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.600 ------------------------------------------------------------------------------- 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 : 19.29 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (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 ARG 0.009 0.001 ARG C 64 TYR 0.054 0.002 TYR B 168 PHE 0.045 0.002 PHE A 354 TRP 0.077 0.006 TRP B 342 HIS 0.011 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00475 (14910) covalent geometry : angle 0.92138 (20230) hydrogen bonds : bond 0.17471 ( 698) hydrogen bonds : angle 7.18406 ( 1809) 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 : 0.556 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: 0.0989 time to fit residues: 85.2849 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 : 0.412 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3425 r_free = 0.3425 target = 0.115126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.099106 restraints weight = 30920.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.102436 restraints weight = 15619.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.104713 restraints weight = 9484.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.106195 restraints weight = 6511.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.107291 restraints weight = 4933.027| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14912 Z= 0.147 Angle : 0.725 8.946 20230 Z= 0.352 Chirality : 0.047 0.173 2230 Planarity : 0.005 0.069 2590 Dihedral : 10.444 173.383 2090 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.05 % Allowed : 26.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.20), residues: 1840 helix: -0.18 (0.19), residues: 745 sheet: 0.28 (0.28), residues: 350 loop : 0.21 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 212 TYR 0.020 0.002 TYR A 168 PHE 0.015 0.001 PHE A 225 TRP 0.041 0.003 TRP B 342 HIS 0.006 0.001 HIS C 90 Details of bonding type rmsd covalent geometry : bond 0.00331 (14910) covalent geometry : angle 0.72549 (20230) hydrogen bonds : bond 0.03722 ( 698) hydrogen bonds : angle 5.44261 ( 1809) Misc. bond : bond 0.00189 ( 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 624 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 561 time to evaluate : 0.557 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: 0.7703 (tp-100) cc_final: 0.7212 (tp-100) REVERT: A 103 HIS cc_start: 0.8356 (m90) cc_final: 0.8026 (m90) REVERT: A 113 ASN cc_start: 0.8888 (m-40) cc_final: 0.8647 (t0) REVERT: A 142 LEU cc_start: 0.9247 (mt) cc_final: 0.8802 (mt) REVERT: A 145 TYR cc_start: 0.8156 (m-80) cc_final: 0.7261 (m-10) REVERT: A 212 ARG cc_start: 0.8414 (ttp80) cc_final: 0.8211 (tmm-80) REVERT: B 80 ASN cc_start: 0.8721 (t0) cc_final: 0.8456 (t0) REVERT: B 84 MET cc_start: 0.8341 (tpp) cc_final: 0.7065 (tpp) REVERT: B 88 TRP cc_start: 0.9362 (m-90) cc_final: 0.8760 (m-90) REVERT: B 115 LYS cc_start: 0.8902 (mmtp) cc_final: 0.8680 (mmmt) REVERT: B 119 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8432 (mt-10) REVERT: B 123 GLN cc_start: 0.9129 (tt0) cc_final: 0.8365 (tp40) REVERT: B 134 MET cc_start: 0.8756 (ppp) cc_final: 0.8471 (tmm) REVERT: B 208 ARG cc_start: 0.8428 (ttp80) cc_final: 0.8138 (ttm-80) REVERT: B 223 LEU cc_start: 0.9051 (tt) cc_final: 0.8714 (tp) REVERT: B 272 GLU cc_start: 0.7505 (tt0) cc_final: 0.7259 (tt0) REVERT: B 316 GLN cc_start: 0.9096 (tm-30) cc_final: 0.8782 (tm-30) REVERT: C 171 TYR cc_start: 0.8459 (m-10) cc_final: 0.8122 (m-10) REVERT: C 248 GLN cc_start: 0.8771 (tt0) cc_final: 0.8064 (mt0) REVERT: C 286 LYS cc_start: 0.8979 (ttmm) cc_final: 0.8668 (mtpp) REVERT: C 327 MET cc_start: 0.8183 (mmt) cc_final: 0.7802 (mmm) REVERT: C 339 TYR cc_start: 0.8575 (m-80) cc_final: 0.8153 (m-10) REVERT: C 342 TRP cc_start: 0.7990 (t60) cc_final: 0.6921 (t60) REVERT: D 80 ASN cc_start: 0.8572 (t0) cc_final: 0.8358 (t0) REVERT: D 118 ARG cc_start: 0.8562 (ptt-90) cc_final: 0.8189 (ptt-90) REVERT: D 123 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8378 (tt0) REVERT: D 195 LEU cc_start: 0.9329 (mt) cc_final: 0.9119 (mt) REVERT: D 215 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8712 (tttp) REVERT: D 354 PHE cc_start: 0.8362 (t80) cc_final: 0.8118 (t80) REVERT: E 23 PHE cc_start: 0.8186 (m-80) cc_final: 0.7835 (m-80) REVERT: E 134 MET cc_start: 0.7784 (pmm) cc_final: 0.7426 (pmm) REVERT: E 193 LYS cc_start: 0.9003 (ttmt) cc_final: 0.8765 (ttmm) REVERT: E 209 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8577 (mm-30) REVERT: E 228 GLU cc_start: 0.8601 (tp30) cc_final: 0.8322 (tp30) REVERT: E 238 LEU cc_start: 0.8306 (mt) cc_final: 0.7951 (mt) REVERT: E 258 ARG cc_start: 0.9145 (mtm-85) cc_final: 0.7961 (ttm110) REVERT: E 298 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7466 (t0) REVERT: E 316 GLN cc_start: 0.8643 (tp40) cc_final: 0.8350 (tp40) outliers start: 63 outliers final: 43 residues processed: 587 average time/residue: 0.0991 time to fit residues: 87.6463 Evaluate side-chains 555 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 509 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 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 182 LEU Chi-restraints excluded: chain B residue 188 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 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 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 153 ILE 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 117 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 106 optimal weight: 0.4980 chunk 6 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 ASN C 117 ASN C 355 GLN D 227 ASN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 ASN E 355 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.114646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.098470 restraints weight = 31374.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.101800 restraints weight = 15635.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.104108 restraints weight = 9450.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.105607 restraints weight = 6448.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.106769 restraints weight = 4874.360| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14912 Z= 0.133 Angle : 0.693 7.857 20230 Z= 0.332 Chirality : 0.046 0.171 2230 Planarity : 0.005 0.069 2590 Dihedral : 9.832 178.986 2078 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.24 % Allowed : 26.56 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.20), residues: 1840 helix: -0.06 (0.20), residues: 750 sheet: 0.35 (0.29), residues: 340 loop : 0.26 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 212 TYR 0.022 0.001 TYR A 168 PHE 0.021 0.001 PHE A 354 TRP 0.028 0.002 TRP B 342 HIS 0.005 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00306 (14910) covalent geometry : angle 0.69304 (20230) hydrogen bonds : bond 0.03609 ( 698) hydrogen bonds : angle 5.14670 ( 1809) Misc. bond : bond 0.00111 ( 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 610 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 544 time to evaluate : 0.358 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: 0.7787 (tp-100) cc_final: 0.7326 (tp-100) REVERT: A 70 LYS cc_start: 0.8324 (mmmm) cc_final: 0.7887 (mttp) REVERT: A 103 HIS cc_start: 0.8418 (m90) cc_final: 0.7876 (m90) REVERT: A 113 ASN cc_start: 0.8976 (m-40) cc_final: 0.8628 (t0) REVERT: A 145 TYR cc_start: 0.8061 (m-80) cc_final: 0.7641 (m-10) REVERT: A 209 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8789 (mm-30) REVERT: A 212 ARG cc_start: 0.8521 (ttp80) cc_final: 0.8188 (tmm-80) REVERT: A 224 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.7952 (p0) REVERT: B 64 ARG cc_start: 0.9282 (ptt180) cc_final: 0.8657 (ptm160) REVERT: B 84 MET cc_start: 0.8428 (tpp) cc_final: 0.7413 (tpp) REVERT: B 88 TRP cc_start: 0.9342 (m-10) cc_final: 0.8785 (m-90) REVERT: B 113 ASN cc_start: 0.9180 (t0) cc_final: 0.8784 (t0) REVERT: B 115 LYS cc_start: 0.8910 (mmtp) cc_final: 0.8532 (mmmt) REVERT: B 119 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8452 (mt-10) REVERT: B 134 MET cc_start: 0.8911 (ppp) cc_final: 0.8601 (tmm) REVERT: B 169 GLU cc_start: 0.8866 (mp0) cc_final: 0.8384 (mm-30) REVERT: B 179 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.6607 (ttm170) REVERT: B 208 ARG cc_start: 0.8351 (ttp80) cc_final: 0.8101 (ttm-80) REVERT: B 223 LEU cc_start: 0.9019 (tt) cc_final: 0.8776 (tp) REVERT: B 256 ARG cc_start: 0.8584 (mtm180) cc_final: 0.8233 (mtm180) REVERT: B 272 GLU cc_start: 0.7449 (tt0) cc_final: 0.7116 (tt0) REVERT: B 316 GLN cc_start: 0.9135 (tm-30) cc_final: 0.8670 (tm-30) REVERT: B 331 MET cc_start: 0.8214 (mtt) cc_final: 0.7599 (mtt) REVERT: C 118 ARG cc_start: 0.8831 (mtm180) cc_final: 0.8476 (mtp-110) REVERT: C 121 MET cc_start: 0.9116 (mtp) cc_final: 0.8801 (mtp) REVERT: C 248 GLN cc_start: 0.8779 (tt0) cc_final: 0.8163 (mt0) REVERT: C 286 LYS cc_start: 0.8942 (ttmm) cc_final: 0.8603 (mtpp) REVERT: C 327 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7784 (mmm) REVERT: C 339 TYR cc_start: 0.8572 (m-80) cc_final: 0.8306 (m-10) REVERT: D 46 MET cc_start: 0.6958 (tmm) cc_final: 0.6461 (tmm) REVERT: D 80 ASN cc_start: 0.8494 (t0) cc_final: 0.8211 (t0) REVERT: D 118 ARG cc_start: 0.8772 (ptt-90) cc_final: 0.8545 (ptt-90) REVERT: D 123 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8466 (tt0) REVERT: E 126 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7670 (m-10) REVERT: E 193 LYS cc_start: 0.8956 (ttmt) cc_final: 0.8687 (ttmm) REVERT: E 209 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8316 (mm-30) REVERT: E 212 ARG cc_start: 0.8710 (ttp80) cc_final: 0.7960 (tmm-80) REVERT: E 221 VAL cc_start: 0.9389 (t) cc_final: 0.9172 (m) REVERT: E 228 GLU cc_start: 0.8695 (tp30) cc_final: 0.8272 (tp30) REVERT: E 258 ARG cc_start: 0.9085 (mtm-85) cc_final: 0.7925 (ttm110) REVERT: E 316 GLN cc_start: 0.8615 (tp40) cc_final: 0.8300 (tp40) outliers start: 66 outliers final: 46 residues processed: 574 average time/residue: 0.0952 time to fit residues: 83.1562 Evaluate side-chains 550 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 499 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 262 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 182 LEU 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 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 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 C residue 327 MET 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 123 GLN Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 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 284 ILE 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 160 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 HIS ** B 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 ASN C 355 GLN D 298 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.106961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.091488 restraints weight = 32615.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.094574 restraints weight = 16392.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.096755 restraints weight = 9989.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.098192 restraints weight = 6860.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.099294 restraints weight = 5180.142| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14912 Z= 0.272 Angle : 0.768 13.239 20230 Z= 0.374 Chirality : 0.049 0.172 2230 Planarity : 0.005 0.063 2590 Dihedral : 9.805 166.551 2078 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 6.95 % Allowed : 25.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.20), residues: 1840 helix: -0.18 (0.19), residues: 750 sheet: 0.02 (0.28), residues: 360 loop : 0.23 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 212 TYR 0.021 0.002 TYR A 168 PHE 0.019 0.002 PHE A 354 TRP 0.025 0.002 TRP B 342 HIS 0.007 0.002 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00611 (14910) covalent geometry : angle 0.76840 (20230) hydrogen bonds : bond 0.04010 ( 698) hydrogen bonds : angle 5.31621 ( 1809) Misc. bond : bond 0.00076 ( 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 601 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 493 time to evaluate : 0.544 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: 0.8001 (tp-100) cc_final: 0.7553 (tp-100) REVERT: A 70 LYS cc_start: 0.8642 (mmmm) cc_final: 0.8382 (mmmm) REVERT: A 103 HIS cc_start: 0.8420 (m90) cc_final: 0.7814 (m90) REVERT: A 142 LEU cc_start: 0.9325 (mt) cc_final: 0.8902 (mt) REVERT: A 145 TYR cc_start: 0.8070 (m-80) cc_final: 0.7639 (m-10) REVERT: A 224 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.7964 (p0) REVERT: A 278 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8345 (mp0) REVERT: B 58 ASP cc_start: 0.8852 (t0) cc_final: 0.8589 (t0) REVERT: B 84 MET cc_start: 0.8967 (tpp) cc_final: 0.7879 (tpp) REVERT: B 88 TRP cc_start: 0.9464 (m-10) cc_final: 0.8805 (m-90) REVERT: B 113 ASN cc_start: 0.9238 (t0) cc_final: 0.8387 (t0) REVERT: B 118 ARG cc_start: 0.7877 (ptt180) cc_final: 0.7628 (mtm180) REVERT: B 123 GLN cc_start: 0.9349 (tt0) cc_final: 0.8818 (tp40) REVERT: B 169 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8321 (mm-30) REVERT: B 179 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.6591 (ttm170) REVERT: B 256 ARG cc_start: 0.8685 (mtm180) cc_final: 0.8461 (mtm180) REVERT: B 294 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8256 (t0) REVERT: B 307 MET cc_start: 0.8610 (mtp) cc_final: 0.8386 (mtp) REVERT: B 342 TRP cc_start: 0.8163 (t60) cc_final: 0.7119 (t60) REVERT: C 61 GLN cc_start: 0.8476 (tp-100) cc_final: 0.8194 (tp40) REVERT: C 117 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8520 (t0) REVERT: C 118 ARG cc_start: 0.8849 (mtm180) cc_final: 0.8532 (mtp-110) REVERT: C 121 MET cc_start: 0.9175 (mtp) cc_final: 0.8854 (mtp) REVERT: C 171 TYR cc_start: 0.8532 (m-10) cc_final: 0.8229 (m-10) REVERT: C 229 MET cc_start: 0.8613 (mmt) cc_final: 0.8393 (mmm) REVERT: C 248 GLN cc_start: 0.8795 (tt0) cc_final: 0.8089 (mt0) REVERT: C 288 ASP cc_start: 0.8228 (m-30) cc_final: 0.7940 (m-30) REVERT: C 327 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7732 (mmm) REVERT: C 342 TRP cc_start: 0.8242 (t60) cc_final: 0.7158 (t60) REVERT: C 358 TRP cc_start: 0.8802 (m100) cc_final: 0.8404 (m100) REVERT: D 80 ASN cc_start: 0.8541 (t0) cc_final: 0.8217 (t0) REVERT: D 119 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8198 (mm-30) REVERT: D 123 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8418 (tt0) REVERT: D 225 PHE cc_start: 0.8379 (t80) cc_final: 0.7908 (t80) REVERT: D 327 MET cc_start: 0.8938 (mmm) cc_final: 0.8563 (mmm) REVERT: D 348 LEU cc_start: 0.8730 (tp) cc_final: 0.8507 (tp) REVERT: E 30 ARG cc_start: 0.8434 (mmp80) cc_final: 0.8042 (mmm160) REVERT: E 122 THR cc_start: 0.8839 (m) cc_final: 0.8551 (t) REVERT: E 134 MET cc_start: 0.7997 (pmm) cc_final: 0.7487 (pmm) REVERT: E 179 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8727 (ttt180) REVERT: E 193 LYS cc_start: 0.8973 (ttmt) cc_final: 0.8702 (ttmm) REVERT: E 228 GLU cc_start: 0.8792 (tp30) cc_final: 0.8369 (tp30) REVERT: E 316 GLN cc_start: 0.8656 (tp40) cc_final: 0.8157 (tp40) outliers start: 108 outliers final: 78 residues processed: 536 average time/residue: 0.0944 time to fit residues: 77.3732 Evaluate side-chains 562 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 476 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 272 GLU Chi-restraints excluded: chain A residue 326 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 45 VAL Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 90 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 150 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 205 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 289 ILE 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 94 ASN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 117 ASN 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 262 THR 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 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 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 267 SER Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 347 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 41 optimal weight: 0.0370 chunk 162 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 145 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN A 139 GLN B 14 ASN B 90 HIS C 117 ASN D 14 ASN ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.111705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.095900 restraints weight = 31460.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.099174 restraints weight = 15623.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.101371 restraints weight = 9410.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.102933 restraints weight = 6442.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.104049 restraints weight = 4818.551| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14912 Z= 0.128 Angle : 0.695 9.980 20230 Z= 0.331 Chirality : 0.046 0.160 2230 Planarity : 0.005 0.061 2590 Dihedral : 9.569 163.256 2078 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 5.34 % Allowed : 27.72 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.20), residues: 1840 helix: -0.01 (0.19), residues: 750 sheet: 0.44 (0.29), residues: 335 loop : 0.31 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 212 TYR 0.023 0.001 TYR E 281 PHE 0.013 0.001 PHE A 354 TRP 0.024 0.002 TRP B 342 HIS 0.008 0.001 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00295 (14910) covalent geometry : angle 0.69480 (20230) hydrogen bonds : bond 0.03419 ( 698) hydrogen bonds : angle 5.02426 ( 1809) Misc. bond : bond 0.00040 ( 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 614 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 531 time to evaluate : 0.435 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: 0.8084 (tp-100) cc_final: 0.7685 (tp-100) REVERT: A 70 LYS cc_start: 0.8606 (mmmm) cc_final: 0.8277 (mmmm) REVERT: A 103 HIS cc_start: 0.8433 (m90) cc_final: 0.8003 (m90) REVERT: A 142 LEU cc_start: 0.9237 (mt) cc_final: 0.8795 (mt) REVERT: A 212 ARG cc_start: 0.8427 (ttp80) cc_final: 0.8160 (tmm-80) REVERT: A 224 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8075 (p0) REVERT: B 113 ASN cc_start: 0.9179 (OUTLIER) cc_final: 0.8142 (t0) REVERT: B 119 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8531 (mt-10) REVERT: B 123 GLN cc_start: 0.9267 (tt0) cc_final: 0.8692 (tp-100) REVERT: B 169 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8227 (mm-30) REVERT: B 179 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.6521 (ttm170) REVERT: B 223 LEU cc_start: 0.8964 (tt) cc_final: 0.8677 (tp) REVERT: B 272 GLU cc_start: 0.7548 (tt0) cc_final: 0.7236 (tt0) REVERT: B 294 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8155 (t0) REVERT: B 307 MET cc_start: 0.8534 (mtp) cc_final: 0.8319 (mtp) REVERT: B 357 MET cc_start: 0.8487 (mmm) cc_final: 0.8286 (mtp) REVERT: C 12 CYS cc_start: 0.8824 (t) cc_final: 0.8339 (t) REVERT: C 117 ASN cc_start: 0.8925 (t0) cc_final: 0.8645 (t0) REVERT: C 121 MET cc_start: 0.9248 (mtp) cc_final: 0.8983 (mtp) REVERT: C 225 PHE cc_start: 0.8681 (t80) cc_final: 0.8474 (t80) REVERT: C 248 GLN cc_start: 0.8751 (tt0) cc_final: 0.8099 (mt0) REVERT: C 288 ASP cc_start: 0.8179 (m-30) cc_final: 0.7877 (m-30) REVERT: C 316 GLN cc_start: 0.8864 (tm-30) cc_final: 0.8443 (tm-30) REVERT: C 327 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7675 (mmm) REVERT: C 358 TRP cc_start: 0.8741 (m100) cc_final: 0.8328 (m100) REVERT: D 30 ARG cc_start: 0.7619 (mmm-85) cc_final: 0.7106 (mtp-110) REVERT: D 80 ASN cc_start: 0.8491 (t0) cc_final: 0.8124 (t0) REVERT: D 115 LYS cc_start: 0.8296 (mmtt) cc_final: 0.8021 (mmtm) REVERT: D 118 ARG cc_start: 0.8697 (ptt-90) cc_final: 0.7909 (ptt-90) REVERT: D 123 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8415 (tt0) REVERT: D 175 HIS cc_start: 0.8782 (p90) cc_final: 0.8534 (p90) REVERT: D 195 LEU cc_start: 0.9336 (mt) cc_final: 0.9130 (mt) REVERT: D 225 PHE cc_start: 0.8419 (t80) cc_final: 0.7980 (t80) REVERT: D 316 GLN cc_start: 0.8241 (tm-30) cc_final: 0.7917 (tm-30) REVERT: D 348 LEU cc_start: 0.8573 (tp) cc_final: 0.8314 (tp) REVERT: E 30 ARG cc_start: 0.8397 (mmp80) cc_final: 0.8143 (mmp-170) REVERT: E 122 THR cc_start: 0.8832 (m) cc_final: 0.8493 (t) REVERT: E 126 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7824 (m-10) REVERT: E 191 LEU cc_start: 0.8970 (tp) cc_final: 0.8724 (tt) REVERT: E 193 LYS cc_start: 0.8940 (ttmt) cc_final: 0.8680 (ttmm) REVERT: E 228 GLU cc_start: 0.8811 (tp30) cc_final: 0.8390 (tp30) REVERT: E 278 GLU cc_start: 0.8160 (tm-30) cc_final: 0.6958 (tm-30) REVERT: E 298 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7639 (t0) REVERT: E 316 GLN cc_start: 0.8587 (tp40) cc_final: 0.8119 (tp40) outliers start: 83 outliers final: 56 residues processed: 563 average time/residue: 0.0924 time to fit residues: 80.5980 Evaluate side-chains 568 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 503 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 ASN 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 109 GLU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 355 GLN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 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 108 THR Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 123 GLN 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 255 GLU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 53 ASP 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 284 ILE Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 305 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 146 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 173 optimal weight: 0.6980 chunk 37 optimal weight: 8.9990 chunk 3 optimal weight: 0.0020 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.112814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.097093 restraints weight = 31055.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.100365 restraints weight = 15548.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.102665 restraints weight = 9404.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.104113 restraints weight = 6376.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.105266 restraints weight = 4784.680| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14912 Z= 0.125 Angle : 0.694 9.874 20230 Z= 0.329 Chirality : 0.046 0.189 2230 Planarity : 0.005 0.057 2590 Dihedral : 9.413 160.999 2078 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 5.02 % Allowed : 27.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.20), residues: 1840 helix: 0.07 (0.20), residues: 750 sheet: 0.55 (0.30), residues: 325 loop : 0.31 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 30 TYR 0.022 0.001 TYR A 168 PHE 0.014 0.001 PHE A 354 TRP 0.020 0.002 TRP B 342 HIS 0.007 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00291 (14910) covalent geometry : angle 0.69389 (20230) hydrogen bonds : bond 0.03293 ( 698) hydrogen bonds : angle 4.94157 ( 1809) 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 610 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 532 time to evaluate : 0.619 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: 0.8105 (tp-100) cc_final: 0.7707 (tp-100) REVERT: A 70 LYS cc_start: 0.8605 (mmmm) cc_final: 0.8223 (mmmm) REVERT: A 103 HIS cc_start: 0.8439 (m90) cc_final: 0.8007 (m90) REVERT: A 121 MET cc_start: 0.8979 (mtp) cc_final: 0.8754 (mtp) REVERT: A 142 LEU cc_start: 0.9254 (mt) cc_final: 0.8841 (mt) REVERT: A 212 ARG cc_start: 0.8416 (ttp80) cc_final: 0.8107 (tmm-80) REVERT: B 36 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8567 (mm) REVERT: B 113 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.8175 (t0) REVERT: B 123 GLN cc_start: 0.9271 (tt0) cc_final: 0.8848 (tp40) REVERT: B 159 ASP cc_start: 0.6793 (t0) cc_final: 0.6545 (t0) REVERT: B 169 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8111 (mm-30) REVERT: B 179 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.6588 (ttm170) REVERT: B 208 ARG cc_start: 0.8600 (tpp80) cc_final: 0.8041 (ttm-80) REVERT: B 223 LEU cc_start: 0.8987 (tt) cc_final: 0.8739 (tp) REVERT: B 272 GLU cc_start: 0.7542 (tt0) cc_final: 0.7159 (tt0) REVERT: B 281 TYR cc_start: 0.8889 (t80) cc_final: 0.8255 (t80) REVERT: B 307 MET cc_start: 0.8563 (mtp) cc_final: 0.8356 (mtp) REVERT: C 12 CYS cc_start: 0.8781 (t) cc_final: 0.8353 (t) REVERT: C 117 ASN cc_start: 0.8985 (t0) cc_final: 0.8774 (t0) REVERT: C 121 MET cc_start: 0.9202 (mtp) cc_final: 0.8886 (mtp) REVERT: C 248 GLN cc_start: 0.8770 (tt0) cc_final: 0.8114 (mt0) REVERT: C 288 ASP cc_start: 0.8215 (m-30) cc_final: 0.7915 (m-30) REVERT: C 298 ASN cc_start: 0.8470 (m-40) cc_final: 0.7495 (t0) REVERT: C 316 GLN cc_start: 0.8871 (tm-30) cc_final: 0.8400 (tm-30) REVERT: C 327 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7597 (mmm) REVERT: C 358 TRP cc_start: 0.8701 (m100) cc_final: 0.8317 (m100) REVERT: D 30 ARG cc_start: 0.7597 (mmm-85) cc_final: 0.7070 (mtp-110) REVERT: D 80 ASN cc_start: 0.8559 (t0) cc_final: 0.8196 (t0) REVERT: D 115 LYS cc_start: 0.8255 (mmtt) cc_final: 0.7974 (mmtm) REVERT: D 118 ARG cc_start: 0.8680 (ptt-90) cc_final: 0.7780 (ptt-90) REVERT: D 175 HIS cc_start: 0.8797 (p90) cc_final: 0.8531 (p90) REVERT: D 195 LEU cc_start: 0.9301 (mt) cc_final: 0.9100 (mt) REVERT: D 225 PHE cc_start: 0.8413 (t80) cc_final: 0.8109 (t80) REVERT: D 316 GLN cc_start: 0.8279 (tm-30) cc_final: 0.8033 (tm-30) REVERT: E 30 ARG cc_start: 0.8449 (mmp80) cc_final: 0.8211 (mmp-170) REVERT: E 113 ASN cc_start: 0.8774 (t0) cc_final: 0.8529 (t0) REVERT: E 122 THR cc_start: 0.8783 (m) cc_final: 0.8419 (t) REVERT: E 126 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7803 (m-10) REVERT: E 169 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8709 (mm-30) REVERT: E 191 LEU cc_start: 0.8959 (tp) cc_final: 0.8706 (tt) REVERT: E 193 LYS cc_start: 0.8915 (ttmt) cc_final: 0.8666 (ttmm) REVERT: E 228 GLU cc_start: 0.8774 (tp30) cc_final: 0.8400 (tp30) REVERT: E 278 GLU cc_start: 0.8170 (tm-30) cc_final: 0.6972 (tm-30) REVERT: E 298 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.7885 (t0) REVERT: E 316 GLN cc_start: 0.8566 (tp40) cc_final: 0.7984 (tp40) outliers start: 78 outliers final: 55 residues processed: 561 average time/residue: 0.1057 time to fit residues: 91.6500 Evaluate side-chains 551 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 489 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 88 TRP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 113 ASN 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 289 ILE Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 355 GLN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 59 GLU 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 153 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 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 108 THR Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 187 LEU 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 126 PHE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 305 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 20 optimal weight: 2.9990 chunk 125 optimal weight: 0.0670 chunk 94 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 97 optimal weight: 0.0070 chunk 72 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN C 113 ASN C 117 ASN ** D 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN E 14 ASN E 43 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.114240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.098739 restraints weight = 31022.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.101901 restraints weight = 15721.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.104126 restraints weight = 9602.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105663 restraints weight = 6579.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.106739 restraints weight = 4899.405| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14912 Z= 0.123 Angle : 0.690 8.619 20230 Z= 0.328 Chirality : 0.045 0.191 2230 Planarity : 0.005 0.057 2590 Dihedral : 9.252 157.023 2078 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.89 % Allowed : 28.68 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.20), residues: 1840 helix: 0.19 (0.20), residues: 750 sheet: 0.55 (0.29), residues: 325 loop : 0.31 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 292 TYR 0.024 0.001 TYR E 281 PHE 0.019 0.001 PHE D 354 TRP 0.022 0.002 TRP B 342 HIS 0.006 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00287 (14910) covalent geometry : angle 0.68957 (20230) hydrogen bonds : bond 0.03177 ( 698) hydrogen bonds : angle 4.86179 ( 1809) Misc. bond : bond 0.00046 ( 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 599 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 523 time to evaluate : 0.640 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: A 43 GLN cc_start: 0.8144 (tp-100) cc_final: 0.7774 (tp-100) REVERT: A 70 LYS cc_start: 0.8649 (mmmm) cc_final: 0.8241 (mmmm) REVERT: A 103 HIS cc_start: 0.8401 (m90) cc_final: 0.7995 (m90) REVERT: A 145 TYR cc_start: 0.8264 (m-10) cc_final: 0.7795 (m-80) REVERT: A 149 ARG cc_start: 0.6469 (mtt90) cc_final: 0.6151 (mtt90) REVERT: A 212 ARG cc_start: 0.8415 (ttp80) cc_final: 0.8110 (tmm-80) REVERT: A 224 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8346 (p0) REVERT: A 229 MET cc_start: 0.8485 (mmm) cc_final: 0.8052 (tpp) REVERT: B 64 ARG cc_start: 0.9369 (ptp-170) cc_final: 0.8925 (ptm160) REVERT: B 113 ASN cc_start: 0.9156 (OUTLIER) cc_final: 0.8248 (t0) REVERT: B 118 ARG cc_start: 0.8707 (mtm180) cc_final: 0.8368 (mtm180) REVERT: B 123 GLN cc_start: 0.9214 (tt0) cc_final: 0.8752 (tp40) REVERT: B 149 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7061 (mpp80) REVERT: B 159 ASP cc_start: 0.6712 (t0) cc_final: 0.6426 (t0) REVERT: B 169 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8092 (mm-30) REVERT: B 179 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.6541 (ttm170) REVERT: B 208 ARG cc_start: 0.8529 (tpp80) cc_final: 0.8277 (tpp80) REVERT: B 272 GLU cc_start: 0.7508 (tt0) cc_final: 0.7091 (tt0) REVERT: B 281 TYR cc_start: 0.8851 (t80) cc_final: 0.8295 (t80) REVERT: B 291 ILE cc_start: 0.7716 (pt) cc_final: 0.7493 (mm) REVERT: B 294 ASP cc_start: 0.8560 (m-30) cc_final: 0.7785 (t0) REVERT: B 331 MET cc_start: 0.8330 (mtm) cc_final: 0.7992 (mtm) REVERT: C 12 CYS cc_start: 0.8746 (t) cc_final: 0.8377 (t) REVERT: C 107 LEU cc_start: 0.8893 (mt) cc_final: 0.8689 (mt) REVERT: C 113 ASN cc_start: 0.9039 (OUTLIER) cc_final: 0.8463 (t0) REVERT: C 118 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8481 (mtp180) REVERT: C 121 MET cc_start: 0.9116 (mtp) cc_final: 0.8899 (mtp) REVERT: C 248 GLN cc_start: 0.8755 (tt0) cc_final: 0.8129 (mt0) REVERT: C 288 ASP cc_start: 0.8152 (m-30) cc_final: 0.7892 (m-30) REVERT: C 316 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8406 (tm-30) REVERT: C 327 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7508 (mmm) REVERT: C 339 TYR cc_start: 0.8419 (m-80) cc_final: 0.8106 (m-80) REVERT: D 30 ARG cc_start: 0.7507 (mmm-85) cc_final: 0.6994 (mtp-110) REVERT: D 80 ASN cc_start: 0.8544 (t0) cc_final: 0.8188 (t0) REVERT: D 115 LYS cc_start: 0.8205 (mmtt) cc_final: 0.7466 (ptpp) REVERT: D 225 PHE cc_start: 0.8425 (t80) cc_final: 0.8101 (t80) REVERT: D 316 GLN cc_start: 0.8270 (tm-30) cc_final: 0.8024 (tm-30) REVERT: E 30 ARG cc_start: 0.8465 (mmp80) cc_final: 0.8222 (mmp-170) REVERT: E 43 GLN cc_start: 0.8103 (tp-100) cc_final: 0.7749 (tp-100) REVERT: E 113 ASN cc_start: 0.8703 (t0) cc_final: 0.8372 (t0) REVERT: E 118 ARG cc_start: 0.8245 (ptm160) cc_final: 0.7692 (ttp80) REVERT: E 122 THR cc_start: 0.8782 (m) cc_final: 0.8466 (t) REVERT: E 126 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7832 (m-10) REVERT: E 191 LEU cc_start: 0.8985 (tp) cc_final: 0.8723 (tt) REVERT: E 193 LYS cc_start: 0.8946 (ttmt) cc_final: 0.8702 (ttmm) REVERT: E 228 GLU cc_start: 0.8748 (tp30) cc_final: 0.8382 (tp30) REVERT: E 278 GLU cc_start: 0.8216 (tm-30) cc_final: 0.6973 (tm-30) REVERT: E 298 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.7959 (t0) REVERT: E 316 GLN cc_start: 0.8613 (tp40) cc_final: 0.8060 (tp40) outliers start: 76 outliers final: 52 residues processed: 549 average time/residue: 0.1155 time to fit residues: 96.4678 Evaluate side-chains 554 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 492 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 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 113 ASN Chi-restraints excluded: chain B residue 144 LEU 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 262 THR Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 355 GLN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 59 GLU 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 113 ASN 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 213 ASP Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 327 MET Chi-restraints excluded: chain 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 153 ILE 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 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 284 ILE Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 305 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 81 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN B 248 GLN D 94 ASN ** 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 = 0.3379 r_free = 0.3379 target = 0.111666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.096274 restraints weight = 31401.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.099528 restraints weight = 15620.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.101749 restraints weight = 9387.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.103337 restraints weight = 6325.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.104312 restraints weight = 4648.651| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14912 Z= 0.157 Angle : 0.714 8.917 20230 Z= 0.341 Chirality : 0.047 0.180 2230 Planarity : 0.005 0.056 2590 Dihedral : 9.165 153.119 2075 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 5.34 % Allowed : 28.75 % Favored : 65.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.20), residues: 1840 helix: 0.27 (0.20), residues: 750 sheet: 0.53 (0.29), residues: 325 loop : 0.32 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 30 TYR 0.028 0.002 TYR C 168 PHE 0.028 0.001 PHE A 354 TRP 0.024 0.002 TRP B 342 HIS 0.009 0.001 HIS D 175 Details of bonding type rmsd covalent geometry : bond 0.00365 (14910) covalent geometry : angle 0.71413 (20230) hydrogen bonds : bond 0.03305 ( 698) hydrogen bonds : angle 4.92103 ( 1809) Misc. bond : bond 0.00055 ( 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 598 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 515 time to evaluate : 0.572 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: 0.8180 (tp-100) cc_final: 0.7811 (tp-100) REVERT: A 70 LYS cc_start: 0.8748 (mmmm) cc_final: 0.8390 (mmmm) REVERT: A 103 HIS cc_start: 0.8455 (m90) cc_final: 0.8006 (m90) REVERT: A 121 MET cc_start: 0.8910 (mtp) cc_final: 0.8659 (mtp) REVERT: A 127 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7552 (tm-30) REVERT: A 142 LEU cc_start: 0.9259 (mt) cc_final: 0.8842 (mt) REVERT: A 149 ARG cc_start: 0.6540 (mtt90) cc_final: 0.6159 (mtt90) REVERT: A 212 ARG cc_start: 0.8438 (ttp80) cc_final: 0.8138 (tmm-80) REVERT: A 224 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8316 (p0) REVERT: A 229 MET cc_start: 0.8511 (mmm) cc_final: 0.8028 (tpp) REVERT: A 278 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8453 (mt-10) REVERT: A 354 PHE cc_start: 0.8769 (t80) cc_final: 0.8257 (t80) REVERT: B 113 ASN cc_start: 0.9225 (OUTLIER) cc_final: 0.8358 (t0) REVERT: B 115 LYS cc_start: 0.9003 (mmtp) cc_final: 0.8703 (tptt) REVERT: B 123 GLN cc_start: 0.9342 (tt0) cc_final: 0.8765 (tp-100) REVERT: B 149 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7067 (mpp80) REVERT: B 159 ASP cc_start: 0.6882 (t0) cc_final: 0.6558 (t0) REVERT: B 169 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8090 (mm-30) REVERT: B 179 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.6546 (ttm170) REVERT: B 223 LEU cc_start: 0.9026 (tt) cc_final: 0.8789 (tp) REVERT: B 272 GLU cc_start: 0.7576 (tt0) cc_final: 0.7206 (tt0) REVERT: B 281 TYR cc_start: 0.8878 (t80) cc_final: 0.8264 (t80) REVERT: B 294 ASP cc_start: 0.8642 (m-30) cc_final: 0.7863 (t0) REVERT: C 12 CYS cc_start: 0.8780 (t) cc_final: 0.8318 (t) REVERT: C 168 TYR cc_start: 0.8500 (t80) cc_final: 0.8296 (t80) REVERT: C 229 MET cc_start: 0.8605 (mmt) cc_final: 0.8343 (mmm) REVERT: C 248 GLN cc_start: 0.8793 (tt0) cc_final: 0.8137 (mt0) REVERT: C 288 ASP cc_start: 0.8279 (m-30) cc_final: 0.8033 (m-30) REVERT: C 298 ASN cc_start: 0.8475 (m-40) cc_final: 0.7518 (t0) REVERT: D 30 ARG cc_start: 0.7598 (mmm-85) cc_final: 0.6995 (mtp-110) REVERT: D 80 ASN cc_start: 0.8568 (t0) cc_final: 0.8179 (t0) REVERT: D 118 ARG cc_start: 0.8651 (ptt-90) cc_final: 0.8040 (ptt-90) REVERT: D 177 ILE cc_start: 0.9410 (mt) cc_final: 0.9205 (mp) REVERT: D 225 PHE cc_start: 0.8357 (t80) cc_final: 0.8112 (t80) REVERT: D 316 GLN cc_start: 0.8330 (tm-30) cc_final: 0.8085 (tm-30) REVERT: E 30 ARG cc_start: 0.8519 (mmp80) cc_final: 0.8257 (mmp-170) REVERT: E 43 GLN cc_start: 0.8215 (tp-100) cc_final: 0.7850 (tp-100) REVERT: E 113 ASN cc_start: 0.8715 (t0) cc_final: 0.8340 (t0) REVERT: E 118 ARG cc_start: 0.8270 (ptm160) cc_final: 0.7761 (ttp-170) REVERT: E 122 THR cc_start: 0.8797 (m) cc_final: 0.8475 (t) REVERT: E 126 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7878 (m-10) REVERT: E 169 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8650 (mm-30) REVERT: E 193 LYS cc_start: 0.8935 (ttmt) cc_final: 0.8644 (ttmm) REVERT: E 228 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8397 (tp30) REVERT: E 272 GLU cc_start: 0.5014 (pt0) cc_final: 0.4064 (tt0) REVERT: E 278 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7099 (tm-30) REVERT: E 298 ASN cc_start: 0.8307 (OUTLIER) cc_final: 0.7871 (t0) REVERT: E 316 GLN cc_start: 0.8635 (tp40) cc_final: 0.8073 (tp40) outliers start: 83 outliers final: 59 residues processed: 548 average time/residue: 0.1147 time to fit residues: 95.7105 Evaluate side-chains 565 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 498 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 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 88 TRP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 144 LEU 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 262 THR Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 355 GLN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain 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 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 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 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 284 ILE Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 357 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 71 optimal weight: 0.4980 chunk 153 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 HIS C 61 GLN ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 HIS D 298 ASN D 355 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.105571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.090643 restraints weight = 32867.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.093533 restraints weight = 16653.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.095819 restraints weight = 10225.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.097269 restraints weight = 6933.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.098363 restraints weight = 5138.762| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 14912 Z= 0.284 Angle : 0.818 13.387 20230 Z= 0.397 Chirality : 0.050 0.179 2230 Planarity : 0.005 0.055 2590 Dihedral : 9.486 156.509 2075 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 5.14 % Allowed : 29.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.20), residues: 1840 helix: 0.09 (0.19), residues: 750 sheet: 0.16 (0.29), residues: 345 loop : 0.20 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 30 TYR 0.050 0.002 TYR C 168 PHE 0.027 0.002 PHE A 354 TRP 0.029 0.002 TRP B 342 HIS 0.008 0.002 HIS D 175 Details of bonding type rmsd covalent geometry : bond 0.00639 (14910) covalent geometry : angle 0.81831 (20230) hydrogen bonds : bond 0.03933 ( 698) hydrogen bonds : angle 5.25508 ( 1809) Misc. bond : bond 0.00075 ( 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 579 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 499 time to evaluate : 0.608 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: 0.8240 (tp-100) cc_final: 0.7870 (tp-100) REVERT: A 70 LYS cc_start: 0.8815 (mmmm) cc_final: 0.8529 (mmmm) REVERT: A 103 HIS cc_start: 0.8456 (m90) cc_final: 0.7989 (m90) REVERT: A 121 MET cc_start: 0.8978 (mtp) cc_final: 0.8732 (mtp) REVERT: A 142 LEU cc_start: 0.9390 (mt) cc_final: 0.9018 (mt) REVERT: A 224 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.8562 (p0) REVERT: A 229 MET cc_start: 0.8749 (mmm) cc_final: 0.8302 (tpp) REVERT: B 88 TRP cc_start: 0.9352 (m-10) cc_final: 0.8811 (m-90) REVERT: B 113 ASN cc_start: 0.9303 (t0) cc_final: 0.7882 (t0) REVERT: B 117 ASN cc_start: 0.9021 (t0) cc_final: 0.8707 (t0) REVERT: B 123 GLN cc_start: 0.9329 (tt0) cc_final: 0.8773 (tp-100) REVERT: B 149 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7023 (mpp80) REVERT: B 159 ASP cc_start: 0.7160 (t0) cc_final: 0.6812 (t0) REVERT: B 168 TYR cc_start: 0.8410 (t80) cc_final: 0.8008 (t80) REVERT: B 169 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: B 179 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.6646 (ttm170) REVERT: B 223 LEU cc_start: 0.9034 (tt) cc_final: 0.8808 (tp) REVERT: B 294 ASP cc_start: 0.8761 (m-30) cc_final: 0.8167 (t0) REVERT: B 357 MET cc_start: 0.8647 (mtp) cc_final: 0.8307 (mtm) REVERT: C 12 CYS cc_start: 0.8908 (t) cc_final: 0.8384 (t) REVERT: C 168 TYR cc_start: 0.8676 (t80) cc_final: 0.8404 (t80) REVERT: C 248 GLN cc_start: 0.8808 (tt0) cc_final: 0.8241 (mt0) REVERT: C 255 GLU cc_start: 0.9115 (pm20) cc_final: 0.8826 (pm20) REVERT: C 288 ASP cc_start: 0.8314 (m-30) cc_final: 0.8110 (m-30) REVERT: C 316 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8376 (tm-30) REVERT: D 30 ARG cc_start: 0.7761 (mmm-85) cc_final: 0.7214 (mtp-110) REVERT: D 80 ASN cc_start: 0.8559 (t0) cc_final: 0.8191 (t0) REVERT: D 115 LYS cc_start: 0.8422 (mmtm) cc_final: 0.8209 (tppt) REVERT: D 118 ARG cc_start: 0.8614 (ptt-90) cc_final: 0.8135 (ptt-90) REVERT: D 119 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8190 (mm-30) REVERT: D 225 PHE cc_start: 0.8398 (t80) cc_final: 0.8094 (t80) REVERT: D 316 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8128 (tm-30) REVERT: E 30 ARG cc_start: 0.8525 (mmp80) cc_final: 0.7915 (mmp-170) REVERT: E 43 GLN cc_start: 0.8267 (tp-100) cc_final: 0.7912 (tp-100) REVERT: E 113 ASN cc_start: 0.8708 (t0) cc_final: 0.8455 (t0) REVERT: E 122 THR cc_start: 0.8832 (m) cc_final: 0.8535 (t) REVERT: E 126 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7885 (m-10) REVERT: E 193 LYS cc_start: 0.8994 (ttmt) cc_final: 0.8695 (ttmm) REVERT: E 228 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8394 (tp30) REVERT: E 272 GLU cc_start: 0.5054 (pt0) cc_final: 0.3946 (tt0) REVERT: E 278 GLU cc_start: 0.8533 (tm-30) cc_final: 0.7353 (tm-30) REVERT: E 316 GLN cc_start: 0.8635 (tp40) cc_final: 0.8039 (tp40) outliers start: 80 outliers final: 59 residues processed: 533 average time/residue: 0.1137 time to fit residues: 92.7752 Evaluate side-chains 557 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 492 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 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 186 ASP Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 355 GLN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 188 THR 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 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 153 ILE 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 284 ILE Chi-restraints excluded: chain D residue 315 MET Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 53 ASP 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 243 GLU Chi-restraints excluded: chain E residue 284 ILE 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 49 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 92 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 118 optimal weight: 0.9980 chunk 165 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 0.0970 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 HIS D 139 GLN D 298 ASN E 139 GLN ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.112523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.096816 restraints weight = 31024.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.100110 restraints weight = 15491.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.102347 restraints weight = 9317.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.103960 restraints weight = 6299.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.105070 restraints weight = 4676.034| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3187 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= 0.137 Angle : 0.770 10.703 20230 Z= 0.369 Chirality : 0.047 0.207 2230 Planarity : 0.005 0.058 2590 Dihedral : 9.215 152.044 2075 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.47 % Allowed : 31.77 % Favored : 64.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.20), residues: 1840 helix: 0.23 (0.20), residues: 745 sheet: 0.39 (0.29), residues: 335 loop : 0.28 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 30 TYR 0.050 0.002 TYR C 168 PHE 0.023 0.001 PHE A 225 TRP 0.035 0.002 TRP B 342 HIS 0.012 0.001 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00319 (14910) covalent geometry : angle 0.77019 (20230) hydrogen bonds : bond 0.03442 ( 698) hydrogen bonds : angle 4.97222 ( 1809) Misc. bond : bond 0.00041 ( 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 606 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 552 time to evaluate : 0.691 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: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8202 (tp-100) cc_final: 0.7967 (tp-100) REVERT: A 70 LYS cc_start: 0.8769 (mmmm) cc_final: 0.8428 (mmmm) REVERT: A 103 HIS cc_start: 0.8427 (m90) cc_final: 0.7993 (m90) REVERT: A 121 MET cc_start: 0.8900 (mtp) cc_final: 0.8637 (mtp) REVERT: A 142 LEU cc_start: 0.9301 (mt) cc_final: 0.8890 (mt) REVERT: A 212 ARG cc_start: 0.8411 (ttp80) cc_final: 0.8112 (tmm-80) REVERT: A 229 MET cc_start: 0.8318 (mmm) cc_final: 0.7995 (tpp) REVERT: A 254 ASN cc_start: 0.9220 (p0) cc_final: 0.8867 (p0) REVERT: B 88 TRP cc_start: 0.9239 (m-10) cc_final: 0.8763 (m-90) REVERT: B 113 ASN cc_start: 0.9216 (OUTLIER) cc_final: 0.8603 (t0) REVERT: B 115 LYS cc_start: 0.9033 (mmtp) cc_final: 0.8611 (mmtp) REVERT: B 123 GLN cc_start: 0.9291 (tt0) cc_final: 0.8814 (tp40) REVERT: B 149 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7053 (mpp80) REVERT: B 159 ASP cc_start: 0.6774 (t0) cc_final: 0.6423 (t0) REVERT: B 281 TYR cc_start: 0.8895 (t80) cc_final: 0.8254 (t80) REVERT: B 294 ASP cc_start: 0.8712 (m-30) cc_final: 0.8034 (t0) REVERT: B 331 MET cc_start: 0.8512 (mtm) cc_final: 0.8208 (mtm) REVERT: B 339 TYR cc_start: 0.8793 (m-80) cc_final: 0.7896 (m-80) REVERT: B 342 TRP cc_start: 0.7820 (t60) cc_final: 0.7278 (t60) REVERT: B 357 MET cc_start: 0.8556 (mtp) cc_final: 0.8191 (mtm) REVERT: C 12 CYS cc_start: 0.8803 (t) cc_final: 0.8388 (t) REVERT: C 14 ASN cc_start: 0.8226 (m-40) cc_final: 0.7675 (m-40) REVERT: C 113 ASN cc_start: 0.9013 (t0) cc_final: 0.8430 (t0) REVERT: C 248 GLN cc_start: 0.8722 (tt0) cc_final: 0.8066 (mt0) REVERT: C 255 GLU cc_start: 0.9032 (pm20) cc_final: 0.8774 (pm20) REVERT: C 288 ASP cc_start: 0.8199 (m-30) cc_final: 0.7986 (m-30) REVERT: C 298 ASN cc_start: 0.8422 (m-40) cc_final: 0.7369 (t0) REVERT: D 30 ARG cc_start: 0.7606 (mmm-85) cc_final: 0.7112 (mtp-110) REVERT: D 80 ASN cc_start: 0.8522 (t0) cc_final: 0.8175 (t0) REVERT: D 115 LYS cc_start: 0.8322 (mmtm) cc_final: 0.8115 (tppt) REVERT: D 118 ARG cc_start: 0.8618 (ptt-90) cc_final: 0.8083 (ptt-90) REVERT: D 318 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8678 (mm-30) REVERT: E 30 ARG cc_start: 0.8532 (mmp80) cc_final: 0.8122 (mmp-170) REVERT: E 43 GLN cc_start: 0.8242 (tp-100) cc_final: 0.7875 (tp-100) REVERT: E 113 ASN cc_start: 0.8695 (t0) cc_final: 0.8461 (t0) REVERT: E 122 THR cc_start: 0.8809 (m) cc_final: 0.8491 (t) REVERT: E 126 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7835 (m-10) REVERT: E 169 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8671 (mm-30) REVERT: E 193 LYS cc_start: 0.8937 (ttmt) cc_final: 0.8660 (ttmm) REVERT: E 228 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8361 (tp30) REVERT: E 272 GLU cc_start: 0.4635 (pt0) cc_final: 0.3632 (tt0) REVERT: E 278 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7150 (tm-30) REVERT: E 298 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8189 (t0) REVERT: E 316 GLN cc_start: 0.8630 (tp40) cc_final: 0.8228 (tp40) REVERT: E 327 MET cc_start: 0.6228 (mmt) cc_final: 0.5150 (mmt) outliers start: 54 outliers final: 43 residues processed: 575 average time/residue: 0.1059 time to fit residues: 93.9942 Evaluate side-chains 565 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 517 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 113 ASN 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 289 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 355 GLN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 315 MET Chi-restraints excluded: chain E residue 53 ASP 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 228 GLU Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 305 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 62 optimal weight: 0.3980 chunk 63 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 131 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN A 373 HIS B 113 ASN ** D 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN E 139 GLN ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.112493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.096638 restraints weight = 30960.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.099963 restraints weight = 15561.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.102234 restraints weight = 9386.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.103795 restraints weight = 6397.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.104918 restraints weight = 4763.409| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.231 14912 Z= 0.223 Angle : 0.936 59.200 20230 Z= 0.500 Chirality : 0.054 1.247 2230 Planarity : 0.005 0.057 2590 Dihedral : 9.233 152.037 2075 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.22 % Allowed : 32.60 % Favored : 64.18 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.20), residues: 1840 helix: 0.23 (0.20), residues: 745 sheet: 0.40 (0.29), residues: 335 loop : 0.27 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 118 TYR 0.035 0.002 TYR C 168 PHE 0.032 0.002 PHE D 225 TRP 0.041 0.003 TRP C 88 HIS 0.015 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00494 (14910) covalent geometry : angle 0.93630 (20230) hydrogen bonds : bond 0.03448 ( 698) hydrogen bonds : angle 4.97203 ( 1809) Misc. bond : bond 0.00038 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2681.70 seconds wall clock time: 47 minutes 14.88 seconds (2834.88 seconds total)