Starting phenix.real_space_refine on Sun Nov 17 23:18:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ord_17120/11_2024/8ord_17120.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ord_17120/11_2024/8ord_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ord_17120/11_2024/8ord_17120.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ord_17120/11_2024/8ord_17120.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ord_17120/11_2024/8ord_17120.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ord_17120/11_2024/8ord_17120.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 1.102 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 105 5.16 5 C 9195 2.51 5 N 2460 2.21 5 O 2815 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 138 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 14590 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2886 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "B" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2886 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "C" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2886 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "D" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2886 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "E" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2886 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.59, per 1000 atoms: 0.86 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: 4.62 Conformation dependent library (CDL) restraints added in 2.5 seconds 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3400 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 30 sheets defined 51.7% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 removed outlier: 3.677A pdb=" N LYS A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 94 removed outlier: 3.562A pdb=" N MET A 84 " --> pdb=" O ASN A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 103 removed outlier: 3.713A pdb=" N GLU A 102 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.955A pdb=" N ARG A 118 " --> pdb=" O PRO A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 147 Processing helix chain 'A' and resid 174 through 177 Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.668A pdb=" N THR A 196 " --> pdb=" O MET A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 204 through 219 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 254 through 259 removed outlier: 3.697A pdb=" N CYS A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 291 through 297 Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.603A pdb=" N THR A 306 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 339 through 351 removed outlier: 3.540A pdb=" N GLY A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 355 Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.650A pdb=" N GLU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.858A pdb=" N VAL A 372 " --> pdb=" O PRO A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 80 through 94 removed outlier: 3.566A pdb=" N MET B 84 " --> pdb=" O ASN B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 103 removed outlier: 3.939A pdb=" N GLU B 102 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 128 removed outlier: 4.115A pdb=" N ARG B 118 " --> pdb=" O PRO B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 147 Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 183 through 196 removed outlier: 3.655A pdb=" N THR B 196 " --> pdb=" O MET B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 199 No H-bonds generated for 'chain 'B' and resid 197 through 199' Processing helix chain 'B' and resid 204 through 219 removed outlier: 3.804A pdb=" N GLU B 209 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS B 219 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 235 removed outlier: 3.614A pdb=" N GLU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 262 removed outlier: 3.634A pdb=" N CYS B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Proline residue: B 260 - end of helix Processing helix chain 'B' and resid 263 through 264 No H-bonds generated for 'chain 'B' and resid 263 through 264' Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 275 through 286 Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 291 through 297 Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.566A pdb=" N THR B 306 " --> pdb=" O GLY B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 323 Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 339 through 349 removed outlier: 4.156A pdb=" N GLY B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B 346 " --> pdb=" O TRP B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 removed outlier: 6.233A pdb=" N THR B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 368 removed outlier: 3.788A pdb=" N GLU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 375 removed outlier: 4.146A pdb=" N ARG B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS B 375 " --> pdb=" O ILE B 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 370 through 375' Processing helix chain 'C' and resid 57 through 63 removed outlier: 3.761A pdb=" N LYS C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 94 removed outlier: 3.777A pdb=" N MET C 84 " --> pdb=" O ASN C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 103 Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.905A pdb=" N ARG C 118 " --> pdb=" O PRO C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 147 Processing helix chain 'C' and resid 174 through 177 Processing helix chain 'C' and resid 183 through 196 removed outlier: 3.945A pdb=" N THR C 196 " --> pdb=" O MET C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 199 No H-bonds generated for 'chain 'C' and resid 197 through 199' Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.530A pdb=" N ILE C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 235 Processing helix chain 'C' and resid 254 through 259 removed outlier: 3.694A pdb=" N CYS C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 265 through 269 Processing helix chain 'C' and resid 275 through 286 Processing helix chain 'C' and resid 288 through 290 No H-bonds generated for 'chain 'C' and resid 288 through 290' Processing helix chain 'C' and resid 291 through 297 Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 310 through 323 Processing helix chain 'C' and resid 336 through 338 No H-bonds generated for 'chain 'C' and resid 336 through 338' Processing helix chain 'C' and resid 339 through 350 removed outlier: 3.778A pdb=" N GLY C 345 " --> pdb=" O VAL C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 355 Processing helix chain 'C' and resid 361 through 368 removed outlier: 3.577A pdb=" N GLU C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 375 removed outlier: 3.712A pdb=" N VAL C 372 " --> pdb=" O PRO C 369 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS C 373 " --> pdb=" O SER C 370 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS C 375 " --> pdb=" O VAL C 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 63 removed outlier: 3.694A pdb=" N LYS D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 94 Processing helix chain 'D' and resid 99 through 103 Processing helix chain 'D' and resid 114 through 128 removed outlier: 3.854A pdb=" N ARG D 118 " --> pdb=" O PRO D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 147 Processing helix chain 'D' and resid 174 through 177 removed outlier: 3.635A pdb=" N ILE D 177 " --> pdb=" O PRO D 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 174 through 177' Processing helix chain 'D' and resid 183 through 196 removed outlier: 4.019A pdb=" N THR D 196 " --> pdb=" O MET D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 199 No H-bonds generated for 'chain 'D' and resid 197 through 199' Processing helix chain 'D' and resid 204 through 219 removed outlier: 3.774A pdb=" N GLU D 209 " --> pdb=" O THR D 205 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 235 Processing helix chain 'D' and resid 254 through 259 removed outlier: 3.815A pdb=" N CYS D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 265 through 270 Processing helix chain 'D' and resid 275 through 286 Processing helix chain 'D' and resid 288 through 290 No H-bonds generated for 'chain 'D' and resid 288 through 290' Processing helix chain 'D' and resid 291 through 297 Processing helix chain 'D' and resid 303 through 307 Processing helix chain 'D' and resid 310 through 323 Processing helix chain 'D' and resid 336 through 338 No H-bonds generated for 'chain 'D' and resid 336 through 338' Processing helix chain 'D' and resid 339 through 349 removed outlier: 3.659A pdb=" N GLY D 345 " --> pdb=" O VAL D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 355 removed outlier: 6.030A pdb=" N THR D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 368 removed outlier: 3.606A pdb=" N GLU D 366 " --> pdb=" O ASP D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 376 removed outlier: 3.713A pdb=" N ARG D 374 " --> pdb=" O SER D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 63 Processing helix chain 'E' and resid 80 through 94 Processing helix chain 'E' and resid 99 through 103 removed outlier: 3.629A pdb=" N GLU E 102 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 128 removed outlier: 4.093A pdb=" N ARG E 118 " --> pdb=" O PRO E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 147 Processing helix chain 'E' and resid 174 through 177 Processing helix chain 'E' and resid 183 through 196 removed outlier: 3.751A pdb=" N THR E 196 " --> pdb=" O MET E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 204 through 219 removed outlier: 3.604A pdb=" N CYS E 219 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 235 Processing helix chain 'E' and resid 254 through 262 removed outlier: 3.571A pdb=" N CYS E 259 " --> pdb=" O GLU E 255 " (cutoff:3.500A) Proline residue: E 260 - end of helix Processing helix chain 'E' and resid 263 through 264 No H-bonds generated for 'chain 'E' and resid 263 through 264' Processing helix chain 'E' and resid 265 through 269 Processing helix chain 'E' and resid 275 through 286 Processing helix chain 'E' and resid 291 through 297 Processing helix chain 'E' and resid 303 through 307 Processing helix chain 'E' and resid 310 through 323 Processing helix chain 'E' and resid 336 through 338 No H-bonds generated for 'chain 'E' and resid 336 through 338' Processing helix chain 'E' and resid 339 through 351 removed outlier: 3.884A pdb=" N GLY E 345 " --> pdb=" O VAL E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 357 removed outlier: 3.796A pdb=" N GLN E 356 " --> pdb=" O THR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 368 removed outlier: 3.650A pdb=" N GLU E 366 " --> pdb=" O ASP E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 376 removed outlier: 3.880A pdb=" N ARG E 374 " --> pdb=" O SER E 370 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 34 removed outlier: 6.735A pdb=" N LEU A 10 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N THR A 108 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N CYS A 12 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA5, first strand: chain 'A' and resid 171 through 172 removed outlier: 6.464A pdb=" N ASN A 299 " --> pdb=" O ILE A 332 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 240 through 243 Processing sheet with id=AA7, first strand: chain 'B' and resid 31 through 34 removed outlier: 6.644A pdb=" N LEU B 10 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N THR B 108 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N CYS B 12 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA9, first strand: chain 'B' and resid 73 through 74 Processing sheet with id=AB1, first strand: chain 'B' and resid 171 through 172 Processing sheet with id=AB2, first strand: chain 'B' and resid 171 through 172 removed outlier: 6.500A pdb=" N ASN B 299 " --> pdb=" O ILE B 332 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 240 through 243 Processing sheet with id=AB4, first strand: chain 'C' and resid 31 through 34 removed outlier: 6.504A pdb=" N LEU C 10 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N THR C 108 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N CYS C 12 " --> pdb=" O THR C 108 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 55 through 56 Processing sheet with id=AB6, first strand: chain 'C' and resid 73 through 74 Processing sheet with id=AB7, first strand: chain 'C' and resid 178 through 180 removed outlier: 6.313A pdb=" N ASN C 299 " --> pdb=" O ILE C 332 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 178 through 180 removed outlier: 4.174A pdb=" N GLN D 43 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 240 through 243 Processing sheet with id=AC1, first strand: chain 'D' and resid 31 through 34 removed outlier: 6.594A pdb=" N LEU D 10 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N THR D 108 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N CYS D 12 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 55 through 56 Processing sheet with id=AC3, first strand: chain 'D' and resid 73 through 74 Processing sheet with id=AC4, first strand: chain 'D' and resid 171 through 172 Processing sheet with id=AC5, first strand: chain 'D' and resid 171 through 172 removed outlier: 7.170A pdb=" N VAL D 300 " --> pdb=" O THR D 151 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE D 153 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N SER D 302 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU D 155 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN D 299 " --> pdb=" O ILE D 332 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 240 through 243 Processing sheet with id=AC7, first strand: chain 'E' and resid 31 through 34 removed outlier: 6.520A pdb=" N LEU E 10 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N THR E 108 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N CYS E 12 " --> pdb=" O THR E 108 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 55 through 56 Processing sheet with id=AC9, first strand: chain 'E' and resid 73 through 74 Processing sheet with id=AD1, first strand: chain 'E' and resid 171 through 172 Processing sheet with id=AD2, first strand: chain 'E' and resid 171 through 172 removed outlier: 6.595A pdb=" N ASN E 299 " --> pdb=" O ILE E 332 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 240 through 243 710 hydrogen bonds defined for protein. 1809 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.80 Time building geometry restraints manager: 4.68 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: 0.00 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: 12.120 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: 0.000 Extract box with map and model: 1.390 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 40.390 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 14910 Z= 0.302 Angle : 0.921 16.158 20230 Z= 0.468 Chirality : 0.050 0.181 2230 Planarity : 0.006 0.097 2590 Dihedral : 17.818 176.981 5545 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.58 % Allowed : 32.22 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.19), residues: 1840 helix: -0.60 (0.18), residues: 740 sheet: 0.30 (0.29), residues: 345 loop : 0.06 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.006 TRP B 342 HIS 0.011 0.001 HIS A 90 PHE 0.045 0.002 PHE A 354 TYR 0.054 0.002 TYR B 168 ARG 0.009 0.001 ARG C 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 569 time to evaluate : 2.845 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: 0.2596 time to fit residues: 221.4592 Evaluate side-chains 509 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 503 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 243 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN B 90 HIS B 139 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14910 Z= 0.239 Angle : 0.732 9.166 20230 Z= 0.356 Chirality : 0.047 0.169 2230 Planarity : 0.005 0.069 2590 Dihedral : 10.465 171.497 2090 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.37 % Allowed : 26.05 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.20), residues: 1840 helix: -0.20 (0.19), residues: 745 sheet: 0.27 (0.28), residues: 350 loop : 0.18 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 342 HIS 0.006 0.001 HIS A 277 PHE 0.014 0.001 PHE A 225 TYR 0.018 0.002 TYR B 168 ARG 0.007 0.001 ARG B 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 545 time to evaluate : 1.458 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: 0.7761 (tp-100) cc_final: 0.7247 (tp-100) REVERT: A 103 HIS cc_start: 0.8415 (m90) cc_final: 0.8068 (m90) REVERT: A 142 LEU cc_start: 0.9278 (mt) cc_final: 0.8852 (mt) REVERT: A 145 TYR cc_start: 0.8141 (m-80) cc_final: 0.7269 (m-10) REVERT: A 212 ARG cc_start: 0.8460 (ttp80) cc_final: 0.8250 (tmm-80) REVERT: A 354 PHE cc_start: 0.8649 (t80) cc_final: 0.8273 (t80) REVERT: B 80 ASN cc_start: 0.8743 (t0) cc_final: 0.8478 (t0) REVERT: B 84 MET cc_start: 0.8402 (tpp) cc_final: 0.7149 (tpp) REVERT: B 88 TRP cc_start: 0.9378 (m-90) cc_final: 0.8769 (m-90) REVERT: B 115 LYS cc_start: 0.8913 (mmtp) cc_final: 0.8693 (mmmt) REVERT: B 123 GLN cc_start: 0.9170 (tt0) cc_final: 0.8422 (tp40) REVERT: B 134 MET cc_start: 0.8805 (ppp) cc_final: 0.8538 (tmm) REVERT: B 179 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.6644 (ttm170) REVERT: B 208 ARG cc_start: 0.8448 (ttp80) cc_final: 0.8130 (ttm-80) REVERT: B 272 GLU cc_start: 0.7526 (tt0) cc_final: 0.7276 (tt0) REVERT: B 316 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8849 (tm-30) REVERT: C 248 GLN cc_start: 0.8809 (tt0) cc_final: 0.8081 (mt0) REVERT: C 286 LYS cc_start: 0.8922 (ttmm) cc_final: 0.8621 (mtpp) REVERT: C 327 MET cc_start: 0.8265 (mmt) cc_final: 0.7987 (mmm) REVERT: C 339 TYR cc_start: 0.8664 (m-80) cc_final: 0.8366 (m-10) REVERT: D 123 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8404 (tt0) REVERT: D 215 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8728 (tttp) REVERT: E 23 PHE cc_start: 0.8175 (m-80) cc_final: 0.7829 (m-80) REVERT: E 134 MET cc_start: 0.7799 (pmm) cc_final: 0.7458 (pmm) REVERT: E 191 LEU cc_start: 0.9005 (tp) cc_final: 0.8804 (tp) REVERT: E 193 LYS cc_start: 0.8964 (ttmt) cc_final: 0.8726 (ttmm) REVERT: E 209 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8659 (mm-30) REVERT: E 228 GLU cc_start: 0.8664 (tp30) cc_final: 0.8306 (tp30) REVERT: E 258 ARG cc_start: 0.9144 (mtm-85) cc_final: 0.7975 (ttm110) REVERT: E 298 ASN cc_start: 0.8184 (OUTLIER) cc_final: 0.7499 (t0) outliers start: 68 outliers final: 50 residues processed: 571 average time/residue: 0.2031 time to fit residues: 172.4497 Evaluate side-chains 558 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 504 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 299 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 139 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 166 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN ** B 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 ASN ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 HIS ** 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 299 ASN E 355 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 14910 Z= 0.372 Angle : 0.758 9.975 20230 Z= 0.369 Chirality : 0.049 0.169 2230 Planarity : 0.005 0.067 2590 Dihedral : 9.980 168.412 2078 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 5.92 % Allowed : 26.88 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.20), residues: 1840 helix: -0.23 (0.19), residues: 750 sheet: 0.04 (0.29), residues: 355 loop : 0.21 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 342 HIS 0.006 0.001 HIS E 373 PHE 0.016 0.002 PHE E 354 TYR 0.024 0.002 TYR C 364 ARG 0.008 0.001 ARG E 212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 519 time to evaluate : 2.361 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: A 43 GLN cc_start: 0.7924 (tp-100) cc_final: 0.7431 (tp-100) REVERT: A 70 LYS cc_start: 0.8674 (mmmm) cc_final: 0.8270 (mmmm) REVERT: A 103 HIS cc_start: 0.8449 (m90) cc_final: 0.7872 (m90) REVERT: A 142 LEU cc_start: 0.9354 (mt) cc_final: 0.9005 (mt) REVERT: A 145 TYR cc_start: 0.8146 (m-80) cc_final: 0.7632 (m-10) REVERT: A 224 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8072 (p0) REVERT: B 84 MET cc_start: 0.8732 (tpp) cc_final: 0.7580 (tpp) REVERT: B 88 TRP cc_start: 0.9455 (m-10) cc_final: 0.8815 (m-90) REVERT: B 113 ASN cc_start: 0.9362 (t0) cc_final: 0.8982 (t0) REVERT: B 119 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8687 (mt-10) REVERT: B 123 GLN cc_start: 0.9375 (tt0) cc_final: 0.8954 (tp40) REVERT: B 134 MET cc_start: 0.8980 (ppp) cc_final: 0.8643 (tmm) REVERT: B 169 GLU cc_start: 0.8944 (mp0) cc_final: 0.8519 (mm-30) REVERT: B 208 ARG cc_start: 0.8489 (ttp80) cc_final: 0.8148 (ttm-80) REVERT: B 294 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8321 (t0) REVERT: C 169 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8317 (mm-30) REVERT: C 248 GLN cc_start: 0.8838 (tt0) cc_final: 0.8180 (mt0) REVERT: C 286 LYS cc_start: 0.8966 (ttmm) cc_final: 0.8631 (mtpp) REVERT: C 288 ASP cc_start: 0.8138 (m-30) cc_final: 0.7909 (m-30) REVERT: C 327 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7993 (mmm) REVERT: C 358 TRP cc_start: 0.8715 (m100) cc_final: 0.8244 (m100) REVERT: D 115 LYS cc_start: 0.8455 (mmtt) cc_final: 0.8195 (mmtm) REVERT: D 118 ARG cc_start: 0.8838 (ptt-90) cc_final: 0.8275 (ptt-90) REVERT: D 123 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8419 (tt0) REVERT: D 215 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8754 (tttp) REVERT: E 122 THR cc_start: 0.8787 (m) cc_final: 0.8425 (t) REVERT: E 126 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7866 (m-10) REVERT: E 193 LYS cc_start: 0.9008 (ttmt) cc_final: 0.8715 (ttmm) REVERT: E 212 ARG cc_start: 0.8827 (ttp80) cc_final: 0.8591 (ttp80) REVERT: E 228 GLU cc_start: 0.8795 (tp30) cc_final: 0.8361 (tp30) REVERT: E 316 GLN cc_start: 0.8586 (tp40) cc_final: 0.8266 (tp40) REVERT: E 373 HIS cc_start: 0.7174 (m90) cc_final: 0.6834 (m-70) outliers start: 92 outliers final: 65 residues processed: 561 average time/residue: 0.2667 time to fit residues: 227.2069 Evaluate side-chains 558 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 487 time to evaluate : 1.706 ------------------------------------------------------------------------------- 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 11 VAL Chi-restraints excluded: chain B residue 27 ASP 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 144 LEU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 327 MET Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 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 E residue 91 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 126 PHE 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 187 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 347 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 87 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 0.0270 chunk 113 optimal weight: 0.5980 chunk 168 optimal weight: 0.6980 chunk 178 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 ASN ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 ASN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14910 Z= 0.182 Angle : 0.682 7.937 20230 Z= 0.327 Chirality : 0.046 0.179 2230 Planarity : 0.005 0.061 2590 Dihedral : 9.590 162.892 2078 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 4.63 % Allowed : 28.04 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.20), residues: 1840 helix: -0.04 (0.20), residues: 750 sheet: 0.49 (0.30), residues: 325 loop : 0.34 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 342 HIS 0.005 0.001 HIS C 89 PHE 0.035 0.001 PHE A 354 TYR 0.021 0.001 TYR A 168 ARG 0.007 0.001 ARG E 212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 546 time to evaluate : 1.765 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: A 43 GLN cc_start: 0.7916 (tp-100) cc_final: 0.7346 (tp-100) REVERT: A 70 LYS cc_start: 0.8650 (mmmm) cc_final: 0.8168 (mmmm) REVERT: A 82 ASP cc_start: 0.8520 (m-30) cc_final: 0.8315 (m-30) REVERT: A 103 HIS cc_start: 0.8466 (m90) cc_final: 0.7929 (m90) REVERT: A 142 LEU cc_start: 0.9205 (mt) cc_final: 0.8756 (mt) REVERT: A 145 TYR cc_start: 0.7875 (m-80) cc_final: 0.7555 (m-10) REVERT: A 212 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8164 (tmm-80) REVERT: B 84 MET cc_start: 0.8685 (tpp) cc_final: 0.7422 (tpp) REVERT: B 88 TRP cc_start: 0.9299 (OUTLIER) cc_final: 0.8766 (m-90) REVERT: B 113 ASN cc_start: 0.9328 (t0) cc_final: 0.8879 (t0) REVERT: B 115 LYS cc_start: 0.8955 (mmtt) cc_final: 0.8516 (tptt) REVERT: B 119 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8507 (mt-10) REVERT: B 123 GLN cc_start: 0.9298 (tt0) cc_final: 0.8775 (tp-100) REVERT: B 169 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8257 (mm-30) REVERT: B 208 ARG cc_start: 0.8340 (ttp80) cc_final: 0.8072 (ttm-80) REVERT: B 272 GLU cc_start: 0.7513 (tt0) cc_final: 0.7156 (tt0) REVERT: B 307 MET cc_start: 0.8566 (mtp) cc_final: 0.8362 (mtp) REVERT: B 342 TRP cc_start: 0.8013 (t60) cc_final: 0.6965 (t60) REVERT: B 357 MET cc_start: 0.8618 (mmm) cc_final: 0.8312 (mtp) REVERT: B 358 TRP cc_start: 0.8167 (m-90) cc_final: 0.7729 (m-90) REVERT: C 61 GLN cc_start: 0.8362 (tp-100) cc_final: 0.7997 (tp-100) REVERT: C 248 GLN cc_start: 0.8726 (tt0) cc_final: 0.8105 (mt0) REVERT: C 254 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8472 (p0) REVERT: C 288 ASP cc_start: 0.8120 (m-30) cc_final: 0.7834 (m-30) REVERT: C 327 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7861 (mmm) REVERT: C 358 TRP cc_start: 0.8686 (m100) cc_final: 0.8225 (m100) REVERT: D 30 ARG cc_start: 0.7614 (mmm-85) cc_final: 0.7095 (mtp-110) REVERT: D 118 ARG cc_start: 0.8746 (ptt-90) cc_final: 0.8537 (ptt-90) REVERT: D 123 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8475 (tt0) REVERT: D 215 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8715 (tttp) REVERT: D 254 ASN cc_start: 0.9428 (p0) cc_final: 0.9012 (p0) REVERT: D 257 PHE cc_start: 0.8157 (p90) cc_final: 0.7462 (p90) REVERT: D 316 GLN cc_start: 0.8316 (tm-30) cc_final: 0.7976 (tm-30) REVERT: E 30 ARG cc_start: 0.8418 (mmp80) cc_final: 0.8053 (mmm160) REVERT: E 126 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7845 (m-10) REVERT: E 161 VAL cc_start: 0.9083 (OUTLIER) cc_final: 0.8856 (t) REVERT: E 193 LYS cc_start: 0.8951 (ttmt) cc_final: 0.8685 (ttmm) REVERT: E 228 GLU cc_start: 0.8752 (tp30) cc_final: 0.8410 (tp30) REVERT: E 298 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.7936 (t0) REVERT: E 316 GLN cc_start: 0.8537 (tp40) cc_final: 0.7896 (tp40) outliers start: 72 outliers final: 47 residues processed: 574 average time/residue: 0.2588 time to fit residues: 224.2374 Evaluate side-chains 550 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 494 time to evaluate : 1.802 ------------------------------------------------------------------------------- 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 362 ASP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 88 TRP 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 188 THR 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 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 153 ILE Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 327 MET Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain E residue 18 LEU 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 161 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 305 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN A 139 GLN A 164 ASN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN C 254 ASN ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 E 356 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 14910 Z= 0.439 Angle : 0.795 12.407 20230 Z= 0.388 Chirality : 0.049 0.180 2230 Planarity : 0.005 0.062 2590 Dihedral : 9.747 165.427 2078 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 6.75 % Allowed : 26.95 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.20), residues: 1840 helix: -0.11 (0.19), residues: 750 sheet: -0.06 (0.28), residues: 360 loop : 0.23 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 342 HIS 0.009 0.002 HIS D 175 PHE 0.030 0.002 PHE A 354 TYR 0.023 0.002 TYR A 168 ARG 0.006 0.001 ARG B 118 *********************** 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 597 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 492 time to evaluate : 1.960 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: 0.8150 (tp-100) cc_final: 0.7636 (tp-100) REVERT: A 70 LYS cc_start: 0.8775 (mmmm) cc_final: 0.8415 (mmmm) REVERT: A 103 HIS cc_start: 0.8517 (m90) cc_final: 0.7967 (m90) REVERT: A 118 ARG cc_start: 0.8749 (ptt180) cc_final: 0.8455 (ptt180) REVERT: A 142 LEU cc_start: 0.9380 (mt) cc_final: 0.9040 (mt) REVERT: A 212 ARG cc_start: 0.8563 (ttp80) cc_final: 0.8285 (tmm-80) REVERT: A 224 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8214 (p0) REVERT: A 278 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8341 (mp0) REVERT: A 342 TRP cc_start: 0.7215 (t60) cc_final: 0.6758 (t60) REVERT: B 88 TRP cc_start: 0.9453 (m-10) cc_final: 0.8799 (m-90) REVERT: B 113 ASN cc_start: 0.9444 (t0) cc_final: 0.8341 (t0) REVERT: B 115 LYS cc_start: 0.9001 (mmtt) cc_final: 0.8661 (mmmt) REVERT: B 123 GLN cc_start: 0.9341 (tt0) cc_final: 0.8785 (tp-100) REVERT: B 169 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8302 (mm-30) REVERT: B 179 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.6626 (ttm170) REVERT: B 208 ARG cc_start: 0.8549 (ttp80) cc_final: 0.8153 (ttm-80) REVERT: B 281 TYR cc_start: 0.9025 (t80) cc_final: 0.8525 (t80) REVERT: B 294 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8306 (t0) REVERT: B 357 MET cc_start: 0.8764 (mmm) cc_final: 0.7871 (mmm) REVERT: C 248 GLN cc_start: 0.8796 (tt0) cc_final: 0.8202 (mt0) REVERT: C 254 ASN cc_start: 0.9035 (OUTLIER) cc_final: 0.8697 (p0) REVERT: C 288 ASP cc_start: 0.8289 (m-30) cc_final: 0.8016 (m-30) REVERT: C 358 TRP cc_start: 0.8766 (m100) cc_final: 0.8333 (m100) REVERT: D 30 ARG cc_start: 0.7863 (mmm-85) cc_final: 0.7373 (mtp-110) REVERT: D 115 LYS cc_start: 0.8457 (mmtt) cc_final: 0.8218 (mmtm) REVERT: D 118 ARG cc_start: 0.8906 (ptt-90) cc_final: 0.8329 (ptt-90) REVERT: D 119 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8194 (mm-30) REVERT: D 123 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8483 (tt0) REVERT: D 215 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8784 (tttp) REVERT: D 225 PHE cc_start: 0.8265 (t80) cc_final: 0.7926 (t80) REVERT: D 316 GLN cc_start: 0.8300 (tm-30) cc_final: 0.8051 (tm-30) REVERT: E 23 PHE cc_start: 0.8460 (m-80) cc_final: 0.8154 (m-80) REVERT: E 30 ARG cc_start: 0.8495 (mmp80) cc_final: 0.8111 (mmm160) REVERT: E 43 GLN cc_start: 0.8353 (tp-100) cc_final: 0.7959 (tp-100) REVERT: E 122 THR cc_start: 0.8851 (m) cc_final: 0.8541 (t) REVERT: E 126 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.8024 (m-10) REVERT: E 193 LYS cc_start: 0.9031 (ttmt) cc_final: 0.8756 (ttmm) REVERT: E 228 GLU cc_start: 0.8769 (tp30) cc_final: 0.8382 (tp30) REVERT: E 272 GLU cc_start: 0.5543 (pt0) cc_final: 0.4569 (tt0) REVERT: E 278 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7205 (tm-30) REVERT: E 316 GLN cc_start: 0.8620 (tp40) cc_final: 0.7883 (tp40) outliers start: 105 outliers final: 79 residues processed: 543 average time/residue: 0.2548 time to fit residues: 208.8332 Evaluate side-chains 561 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 474 time to evaluate : 1.805 ------------------------------------------------------------------------------- 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 151 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 223 LEU 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 27 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 355 GLN Chi-restraints excluded: chain C residue 10 LEU 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 144 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain 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 53 ASP Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 53 ASP 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 126 PHE Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 269 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.0570 chunk 161 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 178 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 82 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 ASN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 ASN E 14 ASN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14910 Z= 0.202 Angle : 0.702 9.733 20230 Z= 0.335 Chirality : 0.046 0.163 2230 Planarity : 0.005 0.062 2590 Dihedral : 9.469 161.469 2078 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.82 % Allowed : 29.20 % Favored : 65.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.20), residues: 1840 helix: 0.13 (0.20), residues: 745 sheet: 0.41 (0.29), residues: 335 loop : 0.31 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 342 HIS 0.010 0.001 HIS D 175 PHE 0.022 0.001 PHE A 354 TYR 0.016 0.001 TYR A 145 ARG 0.005 0.001 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 540 time to evaluate : 1.618 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: 0.8175 (tp-100) cc_final: 0.7752 (tp-100) REVERT: A 70 LYS cc_start: 0.8731 (mmmm) cc_final: 0.8358 (mmmm) REVERT: A 103 HIS cc_start: 0.8459 (m90) cc_final: 0.7989 (m90) REVERT: A 118 ARG cc_start: 0.8664 (ptt180) cc_final: 0.8371 (ptt180) REVERT: A 142 LEU cc_start: 0.9299 (mt) cc_final: 0.8885 (mt) REVERT: A 212 ARG cc_start: 0.8472 (ttp80) cc_final: 0.8195 (tmm-80) REVERT: A 278 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8403 (mp0) REVERT: A 327 MET cc_start: 0.8602 (mmp) cc_final: 0.8096 (mmt) REVERT: B 64 ARG cc_start: 0.9405 (ptt180) cc_final: 0.8924 (ptm160) REVERT: B 83 ASP cc_start: 0.8633 (m-30) cc_final: 0.8384 (p0) REVERT: B 88 TRP cc_start: 0.9354 (m-10) cc_final: 0.8832 (m-90) REVERT: B 90 HIS cc_start: 0.8872 (t70) cc_final: 0.8168 (t70) REVERT: B 95 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8408 (mm-30) REVERT: B 113 ASN cc_start: 0.9367 (t0) cc_final: 0.8905 (t0) REVERT: B 119 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8765 (mt-10) REVERT: B 123 GLN cc_start: 0.9254 (tt0) cc_final: 0.8814 (tp40) REVERT: B 159 ASP cc_start: 0.6940 (t0) cc_final: 0.6712 (t0) REVERT: B 169 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8114 (mm-30) REVERT: B 179 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.6601 (ttm170) REVERT: B 208 ARG cc_start: 0.8424 (ttp80) cc_final: 0.8077 (ttm-80) REVERT: B 210 ILE cc_start: 0.9637 (mp) cc_final: 0.9431 (mp) REVERT: B 272 GLU cc_start: 0.7572 (tt0) cc_final: 0.7303 (tt0) REVERT: B 281 TYR cc_start: 0.8897 (t80) cc_final: 0.8329 (t80) REVERT: B 357 MET cc_start: 0.8737 (mmm) cc_final: 0.7841 (mmm) REVERT: C 248 GLN cc_start: 0.8799 (tt0) cc_final: 0.8128 (mt0) REVERT: C 288 ASP cc_start: 0.8254 (m-30) cc_final: 0.7928 (m-30) REVERT: C 358 TRP cc_start: 0.8730 (m100) cc_final: 0.8327 (m100) REVERT: D 30 ARG cc_start: 0.7692 (mmm-85) cc_final: 0.7093 (mtp-110) REVERT: D 115 LYS cc_start: 0.8357 (mmtt) cc_final: 0.8123 (mmtm) REVERT: D 118 ARG cc_start: 0.8808 (ptt-90) cc_final: 0.8284 (ptt-90) REVERT: D 123 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8449 (tt0) REVERT: D 225 PHE cc_start: 0.8413 (t80) cc_final: 0.7943 (t80) REVERT: D 351 LEU cc_start: 0.9048 (mm) cc_final: 0.8756 (mp) REVERT: E 30 ARG cc_start: 0.8560 (mmp80) cc_final: 0.8227 (mmp-170) REVERT: E 43 GLN cc_start: 0.8298 (tp-100) cc_final: 0.7905 (tp-100) REVERT: E 113 ASN cc_start: 0.8636 (t0) cc_final: 0.8333 (t0) REVERT: E 122 THR cc_start: 0.8854 (m) cc_final: 0.8517 (t) REVERT: E 126 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7902 (m-10) REVERT: E 193 LYS cc_start: 0.8957 (ttmt) cc_final: 0.8706 (ttmm) REVERT: E 228 GLU cc_start: 0.8761 (tp30) cc_final: 0.8405 (tp30) REVERT: E 316 GLN cc_start: 0.8656 (tp40) cc_final: 0.7895 (tp40) REVERT: E 327 MET cc_start: 0.5837 (mmt) cc_final: 0.4908 (mmt) outliers start: 75 outliers final: 51 residues processed: 568 average time/residue: 0.2439 time to fit residues: 210.1243 Evaluate side-chains 555 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 500 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 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 362 ASP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 VAL 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 188 THR Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 355 GLN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 83 ASP 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 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 315 MET Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 305 THR 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 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 172 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 150 optimal weight: 0.2980 chunk 99 optimal weight: 0.5980 chunk 178 optimal weight: 0.7980 chunk 111 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN D 42 HIS D 94 ASN D 227 ASN D 355 GLN E 14 ASN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14910 Z= 0.200 Angle : 0.699 8.404 20230 Z= 0.335 Chirality : 0.046 0.195 2230 Planarity : 0.005 0.056 2590 Dihedral : 9.250 157.740 2075 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.44 % Allowed : 29.90 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.20), residues: 1840 helix: 0.10 (0.20), residues: 750 sheet: 0.47 (0.29), residues: 325 loop : 0.32 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 342 HIS 0.010 0.001 HIS D 175 PHE 0.047 0.001 PHE A 354 TYR 0.016 0.001 TYR A 168 ARG 0.006 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 532 time to evaluate : 1.684 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: 0.8187 (tp-100) cc_final: 0.7764 (tp-100) REVERT: A 70 LYS cc_start: 0.8714 (mmmm) cc_final: 0.8349 (mmmm) REVERT: A 103 HIS cc_start: 0.8465 (m90) cc_final: 0.8015 (m90) REVERT: A 118 ARG cc_start: 0.8699 (ptt180) cc_final: 0.8351 (ptt180) REVERT: A 142 LEU cc_start: 0.9244 (mt) cc_final: 0.8851 (mt) REVERT: A 212 ARG cc_start: 0.8448 (ttp80) cc_final: 0.8146 (tmm-80) REVERT: A 224 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8127 (p0) REVERT: A 327 MET cc_start: 0.8619 (mmp) cc_final: 0.8169 (mmt) REVERT: B 64 ARG cc_start: 0.9380 (ptt180) cc_final: 0.8937 (ptm160) REVERT: B 83 ASP cc_start: 0.8602 (m-30) cc_final: 0.8387 (p0) REVERT: B 90 HIS cc_start: 0.8859 (t70) cc_final: 0.8164 (t70) REVERT: B 95 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8407 (mm-30) REVERT: B 113 ASN cc_start: 0.9333 (t0) cc_final: 0.8930 (t0) REVERT: B 119 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8746 (mt-10) REVERT: B 123 GLN cc_start: 0.9328 (tt0) cc_final: 0.8821 (tp40) REVERT: B 149 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.6700 (mpp80) REVERT: B 159 ASP cc_start: 0.6886 (t0) cc_final: 0.6610 (t0) REVERT: B 179 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.6631 (ttm170) REVERT: B 208 ARG cc_start: 0.8357 (ttp80) cc_final: 0.8085 (ttm-80) REVERT: B 210 ILE cc_start: 0.9633 (mp) cc_final: 0.9418 (mp) REVERT: B 256 ARG cc_start: 0.8624 (mtm180) cc_final: 0.8408 (mtm180) REVERT: B 272 GLU cc_start: 0.7542 (tt0) cc_final: 0.7223 (tt0) REVERT: B 281 TYR cc_start: 0.8878 (t80) cc_final: 0.8375 (t80) REVERT: B 357 MET cc_start: 0.8709 (mmm) cc_final: 0.7817 (mmm) REVERT: C 12 CYS cc_start: 0.8733 (t) cc_final: 0.8378 (t) REVERT: C 14 ASN cc_start: 0.7273 (m-40) cc_final: 0.7059 (m-40) REVERT: C 123 GLN cc_start: 0.8652 (tt0) cc_final: 0.8287 (tm-30) REVERT: C 248 GLN cc_start: 0.8756 (tt0) cc_final: 0.8124 (mt0) REVERT: C 288 ASP cc_start: 0.8230 (m-30) cc_final: 0.7916 (m-30) REVERT: C 339 TYR cc_start: 0.8606 (m-80) cc_final: 0.8320 (m-80) REVERT: C 358 TRP cc_start: 0.8731 (m100) cc_final: 0.8343 (m100) REVERT: D 30 ARG cc_start: 0.7639 (mmm-85) cc_final: 0.7090 (mtp-110) REVERT: D 115 LYS cc_start: 0.8258 (mmtt) cc_final: 0.8047 (mmtm) REVERT: D 118 ARG cc_start: 0.8791 (ptt-90) cc_final: 0.8300 (ptt-90) REVERT: D 123 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8469 (tt0) REVERT: D 225 PHE cc_start: 0.8455 (t80) cc_final: 0.8095 (t80) REVERT: D 316 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7814 (tm-30) REVERT: D 351 LEU cc_start: 0.9090 (mm) cc_final: 0.8787 (mp) REVERT: E 30 ARG cc_start: 0.8530 (mmp80) cc_final: 0.8136 (mmp-170) REVERT: E 43 GLN cc_start: 0.8299 (tp-100) cc_final: 0.7912 (tp-100) REVERT: E 113 ASN cc_start: 0.8655 (t0) cc_final: 0.8336 (t0) REVERT: E 122 THR cc_start: 0.8828 (m) cc_final: 0.8467 (t) REVERT: E 126 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7878 (m-10) REVERT: E 193 LYS cc_start: 0.8946 (ttmt) cc_final: 0.8651 (ttmm) REVERT: E 228 GLU cc_start: 0.8738 (tp30) cc_final: 0.8409 (tp30) REVERT: E 272 GLU cc_start: 0.5693 (pt0) cc_final: 0.4558 (tt0) REVERT: E 278 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7007 (tm-30) REVERT: E 298 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.7854 (t0) REVERT: E 316 GLN cc_start: 0.8655 (tp40) cc_final: 0.7806 (tp40) REVERT: E 327 MET cc_start: 0.5934 (mmt) cc_final: 0.4981 (mmt) outliers start: 69 outliers final: 53 residues processed: 555 average time/residue: 0.2740 time to fit residues: 233.4710 Evaluate side-chains 564 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 505 time to evaluate : 2.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 88 TRP Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 355 GLN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 10 LEU 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 298 ASN Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 357 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 16 optimal weight: 0.0770 chunk 140 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 GLN ** B 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 GLN ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14910 Z= 0.198 Angle : 0.705 9.832 20230 Z= 0.337 Chirality : 0.046 0.176 2230 Planarity : 0.005 0.057 2590 Dihedral : 9.127 154.354 2075 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.76 % Allowed : 29.77 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.20), residues: 1840 helix: 0.15 (0.20), residues: 750 sheet: 0.48 (0.29), residues: 325 loop : 0.34 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 342 HIS 0.012 0.001 HIS B 373 PHE 0.049 0.001 PHE A 354 TYR 0.047 0.002 TYR B 168 ARG 0.006 0.001 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 544 time to evaluate : 1.767 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: 0.8172 (tp-100) cc_final: 0.7808 (tp-100) REVERT: A 70 LYS cc_start: 0.8709 (mmmm) cc_final: 0.8341 (mmmm) REVERT: A 103 HIS cc_start: 0.8465 (m90) cc_final: 0.8012 (m90) REVERT: A 118 ARG cc_start: 0.8697 (ptt180) cc_final: 0.8405 (ptt180) REVERT: A 142 LEU cc_start: 0.9274 (mt) cc_final: 0.8895 (mt) REVERT: A 212 ARG cc_start: 0.8442 (ttp80) cc_final: 0.8156 (tmm-80) REVERT: B 64 ARG cc_start: 0.9390 (ptt180) cc_final: 0.8914 (ptm160) REVERT: B 83 ASP cc_start: 0.8602 (m-30) cc_final: 0.8376 (p0) REVERT: B 90 HIS cc_start: 0.8862 (t70) cc_final: 0.7913 (t-90) REVERT: B 95 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8258 (mm-30) REVERT: B 113 ASN cc_start: 0.9318 (t0) cc_final: 0.8985 (t0) REVERT: B 119 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8719 (mt-10) REVERT: B 123 GLN cc_start: 0.9306 (tt0) cc_final: 0.8662 (tp-100) REVERT: B 149 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.6688 (mpp80) REVERT: B 159 ASP cc_start: 0.6833 (t0) cc_final: 0.6522 (t0) REVERT: B 169 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8252 (mp0) REVERT: B 210 ILE cc_start: 0.9637 (mp) cc_final: 0.9391 (mp) REVERT: B 272 GLU cc_start: 0.7545 (tt0) cc_final: 0.7204 (tt0) REVERT: B 281 TYR cc_start: 0.8852 (t80) cc_final: 0.8374 (t80) REVERT: B 357 MET cc_start: 0.8688 (mmm) cc_final: 0.7773 (mmm) REVERT: C 123 GLN cc_start: 0.8615 (tt0) cc_final: 0.8304 (tm-30) REVERT: C 168 TYR cc_start: 0.8456 (t80) cc_final: 0.8219 (t80) REVERT: C 169 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8014 (mp0) REVERT: C 248 GLN cc_start: 0.8733 (tt0) cc_final: 0.8096 (mt0) REVERT: C 288 ASP cc_start: 0.8229 (m-30) cc_final: 0.7937 (m-30) REVERT: C 358 TRP cc_start: 0.8716 (m100) cc_final: 0.8328 (m100) REVERT: D 30 ARG cc_start: 0.7594 (mmm-85) cc_final: 0.7060 (mtp-110) REVERT: D 115 LYS cc_start: 0.8228 (mmtt) cc_final: 0.7376 (ptpp) REVERT: D 118 ARG cc_start: 0.8787 (ptt-90) cc_final: 0.8413 (ptt-90) REVERT: D 195 LEU cc_start: 0.9309 (mt) cc_final: 0.9105 (mt) REVERT: D 225 PHE cc_start: 0.8383 (t80) cc_final: 0.8094 (t80) REVERT: D 316 GLN cc_start: 0.8108 (tm-30) cc_final: 0.7563 (tm-30) REVERT: D 318 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8721 (mm-30) REVERT: D 351 LEU cc_start: 0.9004 (mm) cc_final: 0.8651 (mp) REVERT: E 30 ARG cc_start: 0.8500 (mmp80) cc_final: 0.8081 (mmp-170) REVERT: E 43 GLN cc_start: 0.8300 (tp-100) cc_final: 0.7913 (tp-100) REVERT: E 113 ASN cc_start: 0.8658 (t0) cc_final: 0.8308 (t0) REVERT: E 122 THR cc_start: 0.8749 (m) cc_final: 0.8433 (t) REVERT: E 126 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.7953 (m-10) REVERT: E 191 LEU cc_start: 0.9055 (tp) cc_final: 0.8791 (tt) REVERT: E 193 LYS cc_start: 0.8944 (ttmt) cc_final: 0.8668 (ttmm) REVERT: E 228 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8389 (tp30) REVERT: E 278 GLU cc_start: 0.8253 (tm-30) cc_final: 0.6993 (tm-30) REVERT: E 298 ASN cc_start: 0.8376 (OUTLIER) cc_final: 0.7918 (t0) REVERT: E 316 GLN cc_start: 0.8656 (tp40) cc_final: 0.7849 (tp40) REVERT: E 327 MET cc_start: 0.6036 (mmt) cc_final: 0.5061 (mmt) outliers start: 74 outliers final: 58 residues processed: 566 average time/residue: 0.2576 time to fit residues: 219.8725 Evaluate side-chains 576 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 513 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 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 36 ILE Chi-restraints excluded: chain B residue 88 TRP Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 262 THR 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 37 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 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 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 305 THR Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 228 GLU 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 170 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14910 Z= 0.223 Angle : 0.726 9.524 20230 Z= 0.346 Chirality : 0.046 0.187 2230 Planarity : 0.005 0.055 2590 Dihedral : 9.094 151.963 2075 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.31 % Allowed : 30.29 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.20), residues: 1840 helix: 0.16 (0.20), residues: 745 sheet: 0.45 (0.29), residues: 335 loop : 0.37 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 342 HIS 0.013 0.001 HIS B 373 PHE 0.047 0.001 PHE A 354 TYR 0.032 0.002 TYR B 168 ARG 0.009 0.001 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 526 time to evaluate : 1.739 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: 0.8182 (tp-100) cc_final: 0.7880 (tp-100) REVERT: A 70 LYS cc_start: 0.8710 (mmmm) cc_final: 0.8367 (mmmm) REVERT: A 84 MET cc_start: 0.8101 (tpt) cc_final: 0.7791 (tpt) REVERT: A 103 HIS cc_start: 0.8485 (m90) cc_final: 0.8016 (m90) REVERT: A 118 ARG cc_start: 0.8677 (ptt180) cc_final: 0.8347 (ptt180) REVERT: A 119 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8275 (mm-30) REVERT: A 142 LEU cc_start: 0.9257 (mt) cc_final: 0.8871 (mt) REVERT: A 212 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8152 (tmm-80) REVERT: B 83 ASP cc_start: 0.8652 (m-30) cc_final: 0.8422 (p0) REVERT: B 88 TRP cc_start: 0.9322 (m-10) cc_final: 0.8884 (m-90) REVERT: B 90 HIS cc_start: 0.8876 (t70) cc_final: 0.7950 (t-90) REVERT: B 95 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8283 (mm-30) REVERT: B 113 ASN cc_start: 0.9319 (t0) cc_final: 0.8876 (t0) REVERT: B 119 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8707 (mt-10) REVERT: B 123 GLN cc_start: 0.9307 (tt0) cc_final: 0.8725 (tp-100) REVERT: B 149 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.6757 (mpp80) REVERT: B 159 ASP cc_start: 0.6849 (t0) cc_final: 0.6549 (t0) REVERT: B 169 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8293 (mp0) REVERT: B 179 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.6647 (ttm170) REVERT: B 272 GLU cc_start: 0.7566 (tt0) cc_final: 0.7214 (tt0) REVERT: B 281 TYR cc_start: 0.8846 (t80) cc_final: 0.8371 (t80) REVERT: B 339 TYR cc_start: 0.8823 (m-80) cc_final: 0.8019 (m-80) REVERT: B 357 MET cc_start: 0.8723 (mmm) cc_final: 0.7805 (mmm) REVERT: C 12 CYS cc_start: 0.8920 (t) cc_final: 0.8500 (t) REVERT: C 123 GLN cc_start: 0.8630 (tt0) cc_final: 0.8321 (tm-30) REVERT: C 168 TYR cc_start: 0.8436 (t80) cc_final: 0.8172 (t80) REVERT: C 169 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8034 (mp0) REVERT: C 248 GLN cc_start: 0.8731 (tt0) cc_final: 0.8086 (mt0) REVERT: C 288 ASP cc_start: 0.8254 (m-30) cc_final: 0.7998 (m-30) REVERT: C 358 TRP cc_start: 0.8713 (m100) cc_final: 0.8336 (m100) REVERT: D 30 ARG cc_start: 0.7584 (mmm-85) cc_final: 0.7104 (mtp-110) REVERT: D 115 LYS cc_start: 0.8226 (mmtt) cc_final: 0.7322 (ptpp) REVERT: D 118 ARG cc_start: 0.8816 (ptt-90) cc_final: 0.8096 (ptt-90) REVERT: D 195 LEU cc_start: 0.9315 (mt) cc_final: 0.9109 (mt) REVERT: D 225 PHE cc_start: 0.8369 (t80) cc_final: 0.8123 (t80) REVERT: D 316 GLN cc_start: 0.8093 (tm-30) cc_final: 0.7533 (tm-30) REVERT: D 318 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8744 (mm-30) REVERT: D 351 LEU cc_start: 0.8970 (mm) cc_final: 0.8603 (mp) REVERT: E 30 ARG cc_start: 0.8510 (mmp80) cc_final: 0.8074 (mmp-170) REVERT: E 43 GLN cc_start: 0.8327 (tp-100) cc_final: 0.7942 (tp-100) REVERT: E 122 THR cc_start: 0.8779 (m) cc_final: 0.8490 (t) REVERT: E 191 LEU cc_start: 0.9063 (tp) cc_final: 0.8788 (tt) REVERT: E 193 LYS cc_start: 0.8952 (ttmt) cc_final: 0.8675 (ttmm) REVERT: E 228 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8400 (tp30) REVERT: E 272 GLU cc_start: 0.5100 (pt0) cc_final: 0.3941 (tt0) REVERT: E 278 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7119 (tm-30) REVERT: E 298 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.7923 (t0) REVERT: E 316 GLN cc_start: 0.8711 (tp40) cc_final: 0.8103 (tp40) outliers start: 67 outliers final: 55 residues processed: 552 average time/residue: 0.2540 time to fit residues: 212.1847 Evaluate side-chains 569 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 509 time to evaluate : 1.744 ------------------------------------------------------------------------------- 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 188 THR 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 108 THR Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 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 37 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain 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 E residue 10 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 228 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 chunk 169 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 113 optimal weight: 0.0570 chunk 89 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 HIS ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 HIS D 75 HIS D 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14910 Z= 0.332 Angle : 0.785 11.738 20230 Z= 0.378 Chirality : 0.048 0.184 2230 Planarity : 0.005 0.054 2590 Dihedral : 9.271 152.948 2075 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.37 % Allowed : 30.55 % Favored : 65.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.20), residues: 1840 helix: 0.11 (0.19), residues: 745 sheet: 0.21 (0.29), residues: 345 loop : 0.32 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 342 HIS 0.016 0.002 HIS B 373 PHE 0.044 0.002 PHE A 354 TYR 0.025 0.002 TYR B 168 ARG 0.006 0.001 ARG A 30 ********************** 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 580 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 512 time to evaluate : 2.043 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: 0.8238 (tp-100) cc_final: 0.8003 (tp-100) REVERT: A 70 LYS cc_start: 0.8764 (mmmm) cc_final: 0.8428 (mmmm) REVERT: A 84 MET cc_start: 0.8331 (tpt) cc_final: 0.8019 (tpt) REVERT: A 103 HIS cc_start: 0.8504 (m90) cc_final: 0.8024 (m90) REVERT: A 118 ARG cc_start: 0.8747 (ptt180) cc_final: 0.8455 (ptt180) REVERT: A 119 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8318 (mm-30) REVERT: A 142 LEU cc_start: 0.9240 (mt) cc_final: 0.8813 (mt) REVERT: A 149 ARG cc_start: 0.6591 (mtt90) cc_final: 0.6104 (mtt90) REVERT: A 212 ARG cc_start: 0.8517 (ttp80) cc_final: 0.8243 (tmm-80) REVERT: A 224 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8455 (p0) REVERT: A 332 ILE cc_start: 0.9039 (pt) cc_final: 0.8732 (pt) REVERT: A 342 TRP cc_start: 0.7224 (t60) cc_final: 0.6802 (t60) REVERT: B 83 ASP cc_start: 0.8698 (m-30) cc_final: 0.8479 (p0) REVERT: B 88 TRP cc_start: 0.9402 (m-10) cc_final: 0.8917 (m-90) REVERT: B 90 HIS cc_start: 0.8904 (t70) cc_final: 0.7825 (t-90) REVERT: B 95 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8236 (mm-30) REVERT: B 113 ASN cc_start: 0.9365 (t0) cc_final: 0.8121 (t0) REVERT: B 117 ASN cc_start: 0.8894 (t0) cc_final: 0.8584 (t0) REVERT: B 119 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8744 (mt-10) REVERT: B 123 GLN cc_start: 0.9318 (tt0) cc_final: 0.8782 (tp-100) REVERT: B 149 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.6591 (mpp80) REVERT: B 159 ASP cc_start: 0.7056 (t0) cc_final: 0.6706 (t0) REVERT: B 169 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8378 (mp0) REVERT: B 179 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.6611 (ttm170) REVERT: B 281 TYR cc_start: 0.8921 (t80) cc_final: 0.8362 (t80) REVERT: B 339 TYR cc_start: 0.8846 (m-80) cc_final: 0.8014 (m-80) REVERT: B 357 MET cc_start: 0.8821 (mmm) cc_final: 0.7954 (mmm) REVERT: C 12 CYS cc_start: 0.9013 (t) cc_final: 0.8539 (t) REVERT: C 113 ASN cc_start: 0.9087 (t0) cc_final: 0.8561 (t0) REVERT: C 123 GLN cc_start: 0.8813 (tt0) cc_final: 0.8465 (tm-30) REVERT: C 169 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8172 (mm-30) REVERT: C 248 GLN cc_start: 0.8765 (tt0) cc_final: 0.8184 (mt0) REVERT: C 358 TRP cc_start: 0.8732 (m100) cc_final: 0.8451 (m100) REVERT: D 30 ARG cc_start: 0.7706 (mmm-85) cc_final: 0.7205 (mtp-110) REVERT: D 118 ARG cc_start: 0.8881 (ptt-90) cc_final: 0.8471 (ptt-90) REVERT: D 119 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8055 (mm-30) REVERT: D 225 PHE cc_start: 0.8425 (t80) cc_final: 0.8082 (t80) REVERT: D 316 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7628 (tm-30) REVERT: D 318 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8761 (mm-30) REVERT: D 327 MET cc_start: 0.8899 (mmm) cc_final: 0.8633 (mmm) REVERT: D 351 LEU cc_start: 0.8955 (mm) cc_final: 0.8573 (mp) REVERT: E 43 GLN cc_start: 0.8329 (tp-100) cc_final: 0.7963 (tp-100) REVERT: E 119 GLU cc_start: 0.8865 (tt0) cc_final: 0.8532 (tp30) REVERT: E 122 THR cc_start: 0.8803 (m) cc_final: 0.8505 (t) REVERT: E 126 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7972 (m-10) REVERT: E 193 LYS cc_start: 0.8975 (ttmt) cc_final: 0.8699 (ttmm) REVERT: E 228 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8423 (tp30) REVERT: E 272 GLU cc_start: 0.4826 (pt0) cc_final: 0.3810 (tt0) REVERT: E 278 GLU cc_start: 0.8463 (tm-30) cc_final: 0.7265 (tm-30) REVERT: E 298 ASN cc_start: 0.8376 (OUTLIER) cc_final: 0.7854 (t0) REVERT: E 316 GLN cc_start: 0.8668 (tp40) cc_final: 0.8204 (tp40) outliers start: 68 outliers final: 56 residues processed: 542 average time/residue: 0.2731 time to fit residues: 225.1243 Evaluate side-chains 555 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 492 time to evaluate : 1.877 ------------------------------------------------------------------------------- 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 188 THR 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 108 THR Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 355 GLN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 83 ASP 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 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 238 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 228 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 150 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.095093 restraints weight = 31388.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.098272 restraints weight = 15645.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.100528 restraints weight = 9454.369| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14910 Z= 0.268 Angle : 0.782 11.385 20230 Z= 0.376 Chirality : 0.048 0.189 2230 Planarity : 0.005 0.082 2590 Dihedral : 9.241 151.679 2075 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.69 % Allowed : 31.38 % Favored : 63.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.20), residues: 1840 helix: 0.09 (0.19), residues: 745 sheet: 0.22 (0.29), residues: 345 loop : 0.29 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 342 HIS 0.018 0.001 HIS B 373 PHE 0.046 0.001 PHE A 354 TYR 0.024 0.002 TYR B 168 ARG 0.006 0.001 ARG A 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4155.09 seconds wall clock time: 87 minutes 27.95 seconds (5247.95 seconds total)