Starting phenix.real_space_refine on Tue Dec 31 08:57:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a2y_15108/12_2024/8a2y_15108.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a2y_15108/12_2024/8a2y_15108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a2y_15108/12_2024/8a2y_15108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a2y_15108/12_2024/8a2y_15108.map" model { file = "/net/cci-nas-00/data/ceres_data/8a2y_15108/12_2024/8a2y_15108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a2y_15108/12_2024/8a2y_15108.cif" } resolution = 2.15 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= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 P 15 5.49 5 S 100 5.16 5 C 9170 2.51 5 N 2450 2.21 5 O 3338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15078 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2877 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "B" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 119 Classifications: {'water': 119} Link IDs: {None: 118} Chain: "D" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 114 Classifications: {'water': 114} Link IDs: {None: 113} Chain: "E" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Restraints were copied for chains: C, B, E, D Time building chain proxies: 7.63, per 1000 atoms: 0.51 Number of scatterers: 15078 At special positions: 0 Unit cell: (94.52, 88.265, 192.515, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 S 100 16.00 P 15 15.00 O 3338 8.00 N 2450 7.00 C 9170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.87 Conformation dependent library (CDL) restraints added in 2.0 seconds 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3410 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 30 sheets defined 53.1% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.110A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.741A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.300A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 348 through 349 No H-bonds generated for 'chain 'C' and resid 348 through 349' Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.552A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 364 removed outlier: 3.566A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 372 removed outlier: 4.099A pdb=" N SER C 368 " --> pdb=" O ALA C 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.110A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.741A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 through 262' Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.300A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 348 through 349 No H-bonds generated for 'chain 'A' and resid 348 through 349' Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.552A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 removed outlier: 3.567A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 removed outlier: 4.099A pdb=" N SER A 368 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.110A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.741A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.299A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 348 through 349 No H-bonds generated for 'chain 'B' and resid 348 through 349' Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.551A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 removed outlier: 3.567A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 removed outlier: 4.098A pdb=" N SER B 368 " --> pdb=" O ALA B 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.110A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.741A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 260 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 301 through 306 removed outlier: 4.299A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 348 through 349 No H-bonds generated for 'chain 'D' and resid 348 through 349' Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.551A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 364 removed outlier: 3.566A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 372 removed outlier: 4.098A pdb=" N SER D 368 " --> pdb=" O ALA D 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.111A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.741A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 261 through 262 No H-bonds generated for 'chain 'E' and resid 261 through 262' Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 301 through 306 removed outlier: 4.300A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'E' and resid 348 through 349 No H-bonds generated for 'chain 'E' and resid 348 through 349' Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.551A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 364 removed outlier: 3.566A pdb=" N GLU E 364 " --> pdb=" O GLN E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 372 removed outlier: 4.098A pdb=" N SER E 368 " --> pdb=" O ALA E 365 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.570A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 41 through 42 removed outlier: 4.099A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 41 through 42 removed outlier: 4.099A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.363A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 176 through 178 removed outlier: 4.124A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AA9, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.571A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.571A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.364A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 176 through 178 removed outlier: 4.165A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.571A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.363A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.571A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.363A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 743 hydrogen bonds defined for protein. 1848 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: 5.55 Time building geometry restraints manager: 4.41 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: 4705 1.34 - 1.46: 2571 1.46 - 1.57: 7394 1.57 - 1.69: 15 1.69 - 1.81: 175 Bond restraints: 14860 Sorted by residual: bond pdb=" O4 PO4 C 403 " pdb=" P PO4 C 403 " ideal model delta sigma weight residual 1.568 1.499 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" O4 PO4 D 403 " pdb=" P PO4 D 403 " ideal model delta sigma weight residual 1.568 1.499 0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" O4 PO4 B 403 " pdb=" P PO4 B 403 " ideal model delta sigma weight residual 1.568 1.499 0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" O4 PO4 E 403 " pdb=" P PO4 E 403 " ideal model delta sigma weight residual 1.568 1.500 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" O4 PO4 A 403 " pdb=" P PO4 A 403 " ideal model delta sigma weight residual 1.568 1.500 0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 14855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 19644 1.45 - 2.90: 353 2.90 - 4.35: 133 4.35 - 5.80: 22 5.80 - 7.25: 18 Bond angle restraints: 20170 Sorted by residual: angle pdb=" NE ARG A 372 " pdb=" CZ ARG A 372 " pdb=" NH2 ARG A 372 " ideal model delta sigma weight residual 119.20 121.54 -2.34 9.00e-01 1.23e+00 6.74e+00 angle pdb=" NE ARG B 372 " pdb=" CZ ARG B 372 " pdb=" NH2 ARG B 372 " ideal model delta sigma weight residual 119.20 121.53 -2.33 9.00e-01 1.23e+00 6.71e+00 angle pdb=" NE ARG E 372 " pdb=" CZ ARG E 372 " pdb=" NH2 ARG E 372 " ideal model delta sigma weight residual 119.20 121.53 -2.33 9.00e-01 1.23e+00 6.71e+00 angle pdb=" NE ARG C 372 " pdb=" CZ ARG C 372 " pdb=" NH2 ARG C 372 " ideal model delta sigma weight residual 119.20 121.52 -2.32 9.00e-01 1.23e+00 6.67e+00 angle pdb=" NE ARG B 37 " pdb=" CZ ARG B 37 " pdb=" NH2 ARG B 37 " ideal model delta sigma weight residual 119.20 121.49 -2.29 9.00e-01 1.23e+00 6.49e+00 ... (remaining 20165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.89: 8820 34.89 - 69.77: 80 69.77 - 104.66: 20 104.66 - 139.54: 5 139.54 - 174.42: 5 Dihedral angle restraints: 8930 sinusoidal: 3615 harmonic: 5315 Sorted by residual: dihedral pdb=" O2A ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PA ADP D 401 " pdb=" PB ADP D 401 " ideal model delta sinusoidal sigma weight residual 300.00 125.58 174.42 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 125.59 174.41 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PA ADP E 401 " pdb=" PB ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 125.60 174.40 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 8927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1096 0.029 - 0.058: 723 0.058 - 0.088: 262 0.088 - 0.117: 129 0.117 - 0.146: 30 Chirality restraints: 2240 Sorted by residual: chirality pdb=" C3' ADP A 401 " pdb=" C2' ADP A 401 " pdb=" C4' ADP A 401 " pdb=" O3' ADP A 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" C3' ADP B 401 " pdb=" C2' ADP B 401 " pdb=" C4' ADP B 401 " pdb=" O3' ADP B 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" C3' ADP C 401 " pdb=" C2' ADP C 401 " pdb=" C4' ADP C 401 " pdb=" O3' ADP C 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 2237 not shown) Planarity restraints: 2570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 340 " 0.015 2.00e-02 2.50e+03 7.48e-03 1.40e+00 pdb=" CG TRP D 340 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP D 340 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP D 340 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP D 340 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 340 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 340 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 340 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 340 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 340 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 340 " 0.015 2.00e-02 2.50e+03 7.44e-03 1.38e+00 pdb=" CG TRP C 340 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP C 340 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP C 340 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 340 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 340 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 340 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 340 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 340 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 340 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 340 " 0.015 2.00e-02 2.50e+03 7.41e-03 1.37e+00 pdb=" CG TRP E 340 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP E 340 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP E 340 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP E 340 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 340 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 340 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 340 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 340 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 340 " 0.003 2.00e-02 2.50e+03 ... (remaining 2567 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 785 2.72 - 3.27: 15353 3.27 - 3.81: 27679 3.81 - 4.36: 36180 4.36 - 4.90: 57272 Nonbonded interactions: 137269 Sorted by model distance: nonbonded pdb="CA CA E 402 " pdb=" O4 PO4 E 403 " model vdw 2.177 2.510 nonbonded pdb="CA CA A 402 " pdb=" O4 PO4 A 403 " model vdw 2.177 2.510 nonbonded pdb="CA CA B 402 " pdb=" O4 PO4 B 403 " model vdw 2.177 2.510 nonbonded pdb="CA CA C 402 " pdb=" O4 PO4 C 403 " model vdw 2.177 2.510 nonbonded pdb="CA CA D 402 " pdb=" O4 PO4 D 403 " model vdw 2.178 2.510 ... (remaining 137264 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 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: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 35.410 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 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 0.069 14860 Z= 0.327 Angle : 0.605 7.247 20170 Z= 0.302 Chirality : 0.046 0.146 2240 Planarity : 0.004 0.026 2570 Dihedral : 13.416 174.425 5520 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.64 % Allowed : 3.54 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.01 (0.19), residues: 1800 helix: -1.84 (0.15), residues: 775 sheet: -0.50 (0.25), residues: 335 loop : 1.14 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 79 HIS 0.003 0.001 HIS D 371 PHE 0.010 0.001 PHE B 262 TYR 0.011 0.001 TYR B 143 ARG 0.004 0.001 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 258 time to evaluate : 1.751 Fit side-chains REVERT: C 167 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7753 (mm-30) REVERT: B 123 MET cc_start: 0.8908 (mmt) cc_final: 0.8560 (mmt) REVERT: B 305 MET cc_start: 0.8530 (mmm) cc_final: 0.8329 (mmm) outliers start: 10 outliers final: 2 residues processed: 263 average time/residue: 1.7063 time to fit residues: 484.9896 Evaluate side-chains 201 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 199 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain D residue 66 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 163 optimal weight: 7.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 137 GLN A 314 GLN B 41 GLN B 59 GLN B 353 GLN D 12 ASN D 59 GLN D 92 ASN D 225 ASN D 246 GLN E 353 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14860 Z= 0.213 Angle : 0.628 7.726 20170 Z= 0.308 Chirality : 0.047 0.176 2240 Planarity : 0.004 0.031 2570 Dihedral : 12.093 179.887 2062 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.29 % Allowed : 8.04 % Favored : 90.68 % 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: 0.57 (0.20), residues: 1800 helix: -0.30 (0.18), residues: 775 sheet: -0.19 (0.25), residues: 335 loop : 1.97 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 79 HIS 0.006 0.001 HIS D 161 PHE 0.012 0.001 PHE B 262 TYR 0.013 0.001 TYR C 143 ARG 0.003 0.001 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 215 time to evaluate : 1.659 Fit side-chains REVERT: C 167 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7738 (mm-30) REVERT: B 100 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7087 (pm20) REVERT: B 123 MET cc_start: 0.8900 (mmt) cc_final: 0.8639 (mmt) outliers start: 20 outliers final: 8 residues processed: 221 average time/residue: 1.5463 time to fit residues: 371.5732 Evaluate side-chains 204 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 195 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 176 optimal weight: 0.9980 chunk 145 optimal weight: 8.9990 chunk 162 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 HIS C 246 GLN A 41 GLN B 41 GLN B 161 HIS B 353 GLN D 161 HIS D 162 ASN D 225 ASN D 246 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14860 Z= 0.303 Angle : 0.672 7.977 20170 Z= 0.332 Chirality : 0.050 0.170 2240 Planarity : 0.004 0.037 2570 Dihedral : 12.124 176.028 2060 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.54 % Allowed : 9.07 % Favored : 89.39 % 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: 0.78 (0.20), residues: 1800 helix: 0.08 (0.19), residues: 785 sheet: -0.20 (0.25), residues: 345 loop : 1.91 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 79 HIS 0.006 0.002 HIS B 371 PHE 0.016 0.002 PHE B 262 TYR 0.013 0.002 TYR B 143 ARG 0.006 0.001 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 1.636 Fit side-chains REVERT: C 128 ASN cc_start: 0.8255 (m110) cc_final: 0.7999 (m-40) REVERT: C 167 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7736 (mm-30) REVERT: B 100 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.7128 (pt0) REVERT: B 123 MET cc_start: 0.8890 (mmt) cc_final: 0.8656 (mmt) outliers start: 24 outliers final: 13 residues processed: 218 average time/residue: 1.5759 time to fit residues: 373.3197 Evaluate side-chains 205 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 HIS C 246 GLN A 41 GLN B 41 GLN B 353 GLN D 225 ASN D 246 GLN E 59 GLN E 353 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14860 Z= 0.232 Angle : 0.627 7.689 20170 Z= 0.307 Chirality : 0.047 0.176 2240 Planarity : 0.004 0.034 2570 Dihedral : 11.989 176.151 2060 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.54 % Allowed : 8.87 % Favored : 89.58 % 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: 0.98 (0.20), residues: 1800 helix: 0.28 (0.19), residues: 790 sheet: -0.02 (0.26), residues: 335 loop : 1.92 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 79 HIS 0.004 0.001 HIS B 371 PHE 0.013 0.002 PHE B 262 TYR 0.011 0.001 TYR A 143 ARG 0.004 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 1.762 Fit side-chains REVERT: C 118 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8075 (mppt) REVERT: C 128 ASN cc_start: 0.8229 (m110) cc_final: 0.7972 (m-40) REVERT: C 167 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7719 (mm-30) REVERT: B 100 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7113 (pt0) outliers start: 24 outliers final: 10 residues processed: 214 average time/residue: 1.5756 time to fit residues: 366.4513 Evaluate side-chains 207 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 99 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN B 41 GLN B 353 GLN D 12 ASN D 40 HIS D 225 ASN D 246 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14860 Z= 0.282 Angle : 0.658 7.851 20170 Z= 0.324 Chirality : 0.049 0.175 2240 Planarity : 0.004 0.036 2570 Dihedral : 12.049 175.985 2060 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.86 % Allowed : 8.87 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.20), residues: 1800 helix: 0.35 (0.19), residues: 785 sheet: -0.13 (0.26), residues: 345 loop : 1.96 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 79 HIS 0.005 0.002 HIS B 371 PHE 0.015 0.002 PHE B 262 TYR 0.011 0.001 TYR B 143 ARG 0.004 0.001 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 196 time to evaluate : 1.703 Fit side-chains REVERT: C 118 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8074 (mppt) REVERT: C 128 ASN cc_start: 0.8250 (m110) cc_final: 0.7995 (m-40) REVERT: C 167 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7745 (mm-30) REVERT: B 100 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7120 (pt0) outliers start: 29 outliers final: 14 residues processed: 213 average time/residue: 1.5645 time to fit residues: 362.5212 Evaluate side-chains 207 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 99 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 174 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 80 optimal weight: 0.0670 chunk 14 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN B 41 GLN B 353 GLN D 225 ASN D 246 GLN E 353 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14860 Z= 0.301 Angle : 0.670 7.926 20170 Z= 0.331 Chirality : 0.050 0.173 2240 Planarity : 0.004 0.037 2570 Dihedral : 12.088 176.297 2060 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.80 % Allowed : 9.52 % Favored : 88.68 % 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: 1.01 (0.20), residues: 1800 helix: 0.37 (0.19), residues: 785 sheet: -0.16 (0.26), residues: 345 loop : 1.95 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 79 HIS 0.006 0.002 HIS B 371 PHE 0.016 0.002 PHE B 262 TYR 0.011 0.002 TYR B 143 ARG 0.004 0.001 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 1.736 Fit side-chains REVERT: C 118 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8073 (mppt) REVERT: C 128 ASN cc_start: 0.8258 (m110) cc_final: 0.8018 (m-40) REVERT: C 167 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7744 (mm-30) REVERT: A 100 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7117 (pm20) REVERT: B 64 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.9080 (pp) REVERT: B 100 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7128 (pt0) REVERT: E 314 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7805 (tp40) outliers start: 28 outliers final: 17 residues processed: 214 average time/residue: 1.5415 time to fit residues: 358.8784 Evaluate side-chains 214 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 314 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 97 optimal weight: 0.2980 chunk 173 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN B 41 GLN D 12 ASN D 225 ASN D 246 GLN E 353 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14860 Z= 0.212 Angle : 0.618 7.639 20170 Z= 0.301 Chirality : 0.047 0.178 2240 Planarity : 0.004 0.033 2570 Dihedral : 11.902 175.969 2060 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.67 % Allowed : 9.90 % Favored : 88.42 % 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: 1.10 (0.20), residues: 1800 helix: 0.43 (0.19), residues: 790 sheet: -0.00 (0.26), residues: 335 loop : 1.92 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 79 HIS 0.004 0.001 HIS B 371 PHE 0.012 0.001 PHE B 262 TYR 0.011 0.001 TYR A 294 ARG 0.004 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 1.782 Fit side-chains REVERT: C 118 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8073 (mppt) REVERT: C 128 ASN cc_start: 0.8224 (m110) cc_final: 0.7971 (m-40) REVERT: C 167 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7731 (mm-30) REVERT: A 84 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8576 (mttm) REVERT: E 314 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7797 (tp40) outliers start: 26 outliers final: 13 residues processed: 213 average time/residue: 1.5759 time to fit residues: 364.9541 Evaluate side-chains 206 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 314 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.5980 chunk 69 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 110 optimal weight: 0.7980 chunk 118 optimal weight: 0.0010 chunk 85 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 41 GLN B 41 GLN D 162 ASN D 225 ASN D 246 GLN E 246 GLN E 353 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14860 Z= 0.132 Angle : 0.563 7.009 20170 Z= 0.269 Chirality : 0.044 0.171 2240 Planarity : 0.003 0.035 2570 Dihedral : 11.357 176.712 2060 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.77 % Allowed : 10.87 % Favored : 88.36 % 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: 1.40 (0.20), residues: 1800 helix: 0.65 (0.19), residues: 775 sheet: 0.08 (0.26), residues: 335 loop : 2.12 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 340 HIS 0.004 0.001 HIS E 87 PHE 0.009 0.001 PHE E 31 TYR 0.009 0.001 TYR B 143 ARG 0.005 0.000 ARG D 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 200 time to evaluate : 1.680 Fit side-chains REVERT: C 128 ASN cc_start: 0.8184 (m110) cc_final: 0.7946 (m-40) REVERT: C 167 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7709 (mm-30) REVERT: B 99 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: E 314 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7721 (tp40) outliers start: 12 outliers final: 3 residues processed: 207 average time/residue: 1.5698 time to fit residues: 353.6752 Evaluate side-chains 199 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 194 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain E residue 314 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 1.9990 chunk 166 optimal weight: 0.3980 chunk 151 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 41 GLN B 41 GLN D 12 ASN D 225 ASN D 246 GLN E 59 GLN E 353 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14860 Z= 0.213 Angle : 0.617 7.397 20170 Z= 0.300 Chirality : 0.047 0.175 2240 Planarity : 0.004 0.032 2570 Dihedral : 11.667 178.742 2060 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.71 % Allowed : 11.38 % Favored : 87.91 % 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: 1.35 (0.20), residues: 1800 helix: 0.60 (0.19), residues: 775 sheet: 0.11 (0.27), residues: 325 loop : 2.05 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 79 HIS 0.004 0.001 HIS B 371 PHE 0.012 0.001 PHE B 262 TYR 0.011 0.001 TYR B 143 ARG 0.005 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 196 time to evaluate : 1.777 Fit side-chains REVERT: C 128 ASN cc_start: 0.8205 (m110) cc_final: 0.7965 (m-40) REVERT: C 167 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7713 (mm-30) REVERT: E 314 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7765 (tp40) outliers start: 11 outliers final: 5 residues processed: 200 average time/residue: 1.6023 time to fit residues: 348.1355 Evaluate side-chains 201 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 195 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 314 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 41 GLN B 41 GLN D 225 ASN D 246 GLN E 59 GLN E 353 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14860 Z= 0.179 Angle : 0.599 7.323 20170 Z= 0.289 Chirality : 0.046 0.177 2240 Planarity : 0.003 0.032 2570 Dihedral : 11.563 179.245 2060 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.51 % Allowed : 11.58 % Favored : 87.91 % 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: 1.41 (0.20), residues: 1800 helix: 0.62 (0.19), residues: 775 sheet: 0.13 (0.27), residues: 335 loop : 2.16 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 79 HIS 0.004 0.001 HIS E 87 PHE 0.010 0.001 PHE B 262 TYR 0.010 0.001 TYR B 143 ARG 0.005 0.000 ARG D 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 190 time to evaluate : 1.822 Fit side-chains REVERT: C 128 ASN cc_start: 0.8203 (m110) cc_final: 0.7964 (m-40) REVERT: C 167 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7710 (mm-30) REVERT: E 314 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7745 (tp40) outliers start: 8 outliers final: 5 residues processed: 194 average time/residue: 1.6221 time to fit residues: 341.3973 Evaluate side-chains 196 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 190 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 314 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN B 41 GLN D 225 ASN D 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.121491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.103884 restraints weight = 13832.479| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 0.96 r_work: 0.3028 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14860 Z= 0.279 Angle : 0.664 7.677 20170 Z= 0.326 Chirality : 0.049 0.175 2240 Planarity : 0.004 0.036 2570 Dihedral : 11.861 173.534 2060 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.64 % Allowed : 11.70 % Favored : 87.65 % 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: 1.14 (0.20), residues: 1800 helix: 0.46 (0.19), residues: 790 sheet: 0.05 (0.27), residues: 325 loop : 1.89 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 79 HIS 0.005 0.002 HIS B 371 PHE 0.015 0.002 PHE B 262 TYR 0.011 0.001 TYR B 143 ARG 0.009 0.001 ARG D 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6378.35 seconds wall clock time: 115 minutes 1.75 seconds (6901.75 seconds total)