Starting phenix.real_space_refine on Fri Jun 13 17:49:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a2y_15108/06_2025/8a2y_15108.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a2y_15108/06_2025/8a2y_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_15108/06_2025/8a2y_15108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a2y_15108/06_2025/8a2y_15108.map" model { file = "/net/cci-nas-00/data/ceres_data/8a2y_15108/06_2025/8a2y_15108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a2y_15108/06_2025/8a2y_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-5710/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: 7.74, 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: 3.77 Conformation dependent library (CDL) restraints added in 1.7 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: 2.59 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: 5.19 Time building geometry restraints manager: 4.33 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 4.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 34.990 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 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:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.720 ------------------------------------------------------------------------------- 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= 0.233 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 Details of bonding type rmsd hydrogen bonds : bond 0.21576 ( 728) hydrogen bonds : angle 7.56237 ( 1848) covalent geometry : bond 0.00504 (14860) covalent geometry : angle 0.60503 (20170) *********************** 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 : 1.787 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: 1.6486 time to fit residues: 468.4834 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 : 1.731 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.122555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.104931 restraints weight = 13726.844| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 0.97 r_work: 0.3049 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 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= 0.151 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 Details of bonding type rmsd hydrogen bonds : bond 0.04595 ( 728) hydrogen bonds : angle 5.20046 ( 1848) covalent geometry : bond 0.00326 (14860) covalent geometry : angle 0.62842 (20170) *********************** 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 : 1.823 Fit side-chains REVERT: C 234 SER cc_start: 0.8015 (m) cc_final: 0.7738 (p) REVERT: B 100 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7589 (pm20) REVERT: B 117 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8192 (mt-10) REVERT: B 123 MET cc_start: 0.9064 (mmt) cc_final: 0.8811 (mmt) REVERT: D 25 ASP cc_start: 0.8212 (p0) cc_final: 0.7894 (m-30) REVERT: E 57 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7802 (pt0) outliers start: 20 outliers final: 8 residues processed: 221 average time/residue: 1.5001 time to fit residues: 360.6173 Evaluate side-chains 205 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 195 time to evaluate : 1.674 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain E residue 57 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 17 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 61 optimal weight: 0.0030 chunk 161 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 44 optimal weight: 0.0670 chunk 9 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 overall best weight: 0.4928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN A 41 GLN A 314 GLN B 41 GLN B 353 GLN D 225 ASN D 246 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.125503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.108320 restraints weight = 13816.848| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 0.96 r_work: 0.3105 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1906 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= 0.093 Angle : 0.554 6.924 20170 Z= 0.262 Chirality : 0.044 0.167 2240 Planarity : 0.003 0.032 2570 Dihedral : 11.222 177.535 2060 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.90 % Allowed : 9.84 % 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: 1.12 (0.20), residues: 1800 helix: 0.30 (0.19), residues: 775 sheet: 0.01 (0.26), residues: 335 loop : 2.09 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 79 HIS 0.003 0.001 HIS D 161 PHE 0.008 0.001 PHE C 255 TYR 0.010 0.001 TYR A 143 ARG 0.007 0.000 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.03340 ( 728) hydrogen bonds : angle 4.68486 ( 1848) covalent geometry : bond 0.00191 (14860) covalent geometry : angle 0.55445 (20170) *********************** 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 228 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 214 time to evaluate : 1.726 Fit side-chains REVERT: C 128 ASN cc_start: 0.8470 (m110) cc_final: 0.8199 (m-40) REVERT: C 234 SER cc_start: 0.7898 (m) cc_final: 0.7680 (p) REVERT: B 117 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8116 (mt-10) REVERT: B 123 MET cc_start: 0.9053 (mmt) cc_final: 0.8765 (mmt) REVERT: B 360 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7662 (tm-30) REVERT: D 25 ASP cc_start: 0.8185 (p0) cc_final: 0.7912 (m-30) REVERT: D 234 SER cc_start: 0.7772 (m) cc_final: 0.7536 (p) REVERT: D 324 THR cc_start: 0.8807 (p) cc_final: 0.8579 (t) REVERT: E 234 SER cc_start: 0.8432 (m) cc_final: 0.8074 (p) outliers start: 14 outliers final: 2 residues processed: 222 average time/residue: 1.5861 time to fit residues: 382.1312 Evaluate side-chains 200 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 198 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 96 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 161 HIS C 246 GLN C 353 GLN A 41 GLN A 314 GLN B 41 GLN B 161 HIS B 353 GLN D 40 HIS D 162 ASN D 225 ASN D 246 GLN E 59 GLN E 161 HIS E 353 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.119576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.101826 restraints weight = 13582.702| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 0.96 r_work: 0.3001 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 14860 Z= 0.283 Angle : 0.735 8.014 20170 Z= 0.367 Chirality : 0.054 0.172 2240 Planarity : 0.005 0.050 2570 Dihedral : 12.220 175.346 2060 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.41 % Allowed : 9.07 % Favored : 89.52 % 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: 0.86 (0.20), residues: 1800 helix: 0.20 (0.19), residues: 785 sheet: -0.25 (0.28), residues: 315 loop : 1.85 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP D 340 HIS 0.007 0.002 HIS B 371 PHE 0.020 0.002 PHE B 262 TYR 0.013 0.002 TYR B 143 ARG 0.006 0.001 ARG D 177 Details of bonding type rmsd hydrogen bonds : bond 0.05617 ( 728) hydrogen bonds : angle 5.31340 ( 1848) covalent geometry : bond 0.00641 (14860) covalent geometry : angle 0.73487 (20170) *********************** 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 220 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 1.649 Fit side-chains REVERT: C 128 ASN cc_start: 0.8527 (m110) cc_final: 0.8245 (m-40) REVERT: B 123 MET cc_start: 0.9048 (mmt) cc_final: 0.8824 (mmt) REVERT: B 225 ASN cc_start: 0.8343 (m110) cc_final: 0.8107 (m-40) REVERT: D 25 ASP cc_start: 0.8244 (p0) cc_final: 0.7997 (m-30) REVERT: D 234 SER cc_start: 0.7868 (m) cc_final: 0.7620 (p) REVERT: D 324 THR cc_start: 0.8828 (p) cc_final: 0.8584 (t) outliers start: 22 outliers final: 11 residues processed: 210 average time/residue: 1.5681 time to fit residues: 358.3411 Evaluate side-chains 204 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 193 time to evaluate : 1.633 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 112 optimal weight: 0.0980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 246 GLN A 41 GLN B 41 GLN B 353 GLN D 12 ASN D 225 ASN D 246 GLN E 353 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.121274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.103650 restraints weight = 13853.557| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 0.97 r_work: 0.3030 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14860 Z= 0.165 Angle : 0.634 7.721 20170 Z= 0.311 Chirality : 0.048 0.176 2240 Planarity : 0.004 0.034 2570 Dihedral : 12.025 176.390 2060 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.35 % Allowed : 9.52 % Favored : 89.13 % 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: 1.04 (0.20), residues: 1800 helix: 0.33 (0.19), residues: 790 sheet: -0.01 (0.26), residues: 335 loop : 1.95 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 79 HIS 0.006 0.001 HIS D 161 PHE 0.014 0.002 PHE B 262 TYR 0.011 0.001 TYR B 143 ARG 0.003 0.000 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.04388 ( 728) hydrogen bonds : angle 4.99123 ( 1848) covalent geometry : bond 0.00365 (14860) covalent geometry : angle 0.63412 (20170) *********************** 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 224 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 1.873 Fit side-chains REVERT: C 57 GLU cc_start: 0.8246 (tt0) cc_final: 0.8034 (pt0) REVERT: C 118 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8241 (mppt) REVERT: C 128 ASN cc_start: 0.8491 (m110) cc_final: 0.8208 (m-40) REVERT: B 117 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8191 (mt-10) REVERT: B 225 ASN cc_start: 0.8338 (m110) cc_final: 0.8111 (m-40) REVERT: D 25 ASP cc_start: 0.8233 (p0) cc_final: 0.8003 (m-30) REVERT: D 234 SER cc_start: 0.7861 (m) cc_final: 0.7611 (p) REVERT: D 324 THR cc_start: 0.8821 (p) cc_final: 0.8582 (t) REVERT: E 234 SER cc_start: 0.8438 (m) cc_final: 0.8064 (p) outliers start: 21 outliers final: 11 residues processed: 214 average time/residue: 1.6490 time to fit residues: 384.2092 Evaluate side-chains 204 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 122 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 148 optimal weight: 0.2980 chunk 145 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN A 41 GLN B 41 GLN D 225 ASN D 246 GLN E 353 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.120682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.102825 restraints weight = 13731.986| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 0.97 r_work: 0.3016 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2010 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= 0.197 Angle : 0.664 7.856 20170 Z= 0.328 Chirality : 0.049 0.174 2240 Planarity : 0.004 0.037 2570 Dihedral : 12.085 176.165 2060 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.61 % Allowed : 9.77 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.20), residues: 1800 helix: 0.37 (0.19), residues: 785 sheet: -0.14 (0.25), residues: 345 loop : 1.96 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 79 HIS 0.006 0.002 HIS D 161 PHE 0.015 0.002 PHE B 262 TYR 0.012 0.001 TYR B 143 ARG 0.004 0.001 ARG D 372 Details of bonding type rmsd hydrogen bonds : bond 0.04755 ( 728) hydrogen bonds : angle 5.07915 ( 1848) covalent geometry : bond 0.00441 (14860) covalent geometry : angle 0.66445 (20170) *********************** 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 220 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 1.820 Fit side-chains REVERT: C 57 GLU cc_start: 0.8226 (tt0) cc_final: 0.8017 (pt0) REVERT: C 118 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8233 (mppt) REVERT: C 128 ASN cc_start: 0.8509 (m110) cc_final: 0.8230 (m-40) REVERT: B 64 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.9077 (pp) REVERT: B 99 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: B 100 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7587 (pt0) REVERT: B 117 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8182 (mt-10) REVERT: B 225 ASN cc_start: 0.8348 (m110) cc_final: 0.8129 (m-40) REVERT: D 25 ASP cc_start: 0.8229 (p0) cc_final: 0.8018 (m-30) REVERT: D 234 SER cc_start: 0.7891 (m) cc_final: 0.7641 (p) REVERT: D 324 THR cc_start: 0.8831 (p) cc_final: 0.8591 (t) REVERT: E 234 SER cc_start: 0.8472 (m) cc_final: 0.8092 (p) REVERT: E 350 SER cc_start: 0.8819 (p) cc_final: 0.8587 (m) outliers start: 25 outliers final: 14 residues processed: 212 average time/residue: 1.5357 time to fit residues: 354.4246 Evaluate side-chains 212 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 1.934 ------------------------------------------------------------------------------- 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 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 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 99 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 74 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 152 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.120941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.103158 restraints weight = 13715.126| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 0.97 r_work: 0.3020 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14860 Z= 0.187 Angle : 0.656 7.814 20170 Z= 0.323 Chirality : 0.049 0.175 2240 Planarity : 0.004 0.034 2570 Dihedral : 12.048 176.348 2060 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.74 % Allowed : 9.84 % 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: 1.05 (0.20), residues: 1800 helix: 0.40 (0.19), residues: 785 sheet: -0.14 (0.25), 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 D 161 PHE 0.015 0.002 PHE B 262 TYR 0.011 0.001 TYR B 143 ARG 0.005 0.001 ARG D 372 Details of bonding type rmsd hydrogen bonds : bond 0.04593 ( 728) hydrogen bonds : angle 5.02544 ( 1848) covalent geometry : bond 0.00420 (14860) covalent geometry : angle 0.65559 (20170) *********************** 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 221 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 1.706 Fit side-chains REVERT: C 57 GLU cc_start: 0.8231 (tt0) cc_final: 0.8014 (pt0) REVERT: C 118 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8235 (mppt) REVERT: C 128 ASN cc_start: 0.8493 (m110) cc_final: 0.8215 (m-40) REVERT: A 100 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7707 (pm20) REVERT: B 64 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.9080 (pp) REVERT: B 99 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: B 100 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7579 (pt0) REVERT: B 117 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8171 (mt-10) REVERT: B 225 ASN cc_start: 0.8346 (m110) cc_final: 0.8117 (m-40) REVERT: D 234 SER cc_start: 0.7875 (m) cc_final: 0.7632 (p) REVERT: D 324 THR cc_start: 0.8813 (p) cc_final: 0.8581 (t) REVERT: E 234 SER cc_start: 0.8463 (m) cc_final: 0.8086 (p) REVERT: E 314 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8021 (tp40) REVERT: E 350 SER cc_start: 0.8818 (p) cc_final: 0.8597 (m) outliers start: 27 outliers final: 16 residues processed: 210 average time/residue: 1.7815 time to fit residues: 406.2279 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 : 1.851 ------------------------------------------------------------------------------- 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 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 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 99 GLU 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 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 Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 79 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.122691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.105081 restraints weight = 13675.028| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 0.96 r_work: 0.3053 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14860 Z= 0.128 Angle : 0.600 7.454 20170 Z= 0.291 Chirality : 0.046 0.179 2240 Planarity : 0.003 0.033 2570 Dihedral : 11.808 176.941 2060 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.35 % Allowed : 10.42 % Favored : 88.23 % 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: 1.29 (0.20), residues: 1800 helix: 0.56 (0.19), residues: 775 sheet: 0.04 (0.26), residues: 335 loop : 2.07 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 340 HIS 0.005 0.001 HIS D 161 PHE 0.010 0.001 PHE D 262 TYR 0.010 0.001 TYR A 294 ARG 0.005 0.000 ARG D 372 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 728) hydrogen bonds : angle 4.78108 ( 1848) covalent geometry : bond 0.00277 (14860) covalent geometry : angle 0.59994 (20170) *********************** 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 217 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 1.726 Fit side-chains REVERT: C 118 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8264 (mppt) REVERT: C 128 ASN cc_start: 0.8467 (m110) cc_final: 0.8184 (m-40) REVERT: B 99 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: B 100 GLU cc_start: 0.7820 (pt0) cc_final: 0.7555 (pm20) REVERT: B 117 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8157 (mt-10) REVERT: B 225 ASN cc_start: 0.8334 (m110) cc_final: 0.8108 (m-40) REVERT: D 234 SER cc_start: 0.7788 (m) cc_final: 0.7587 (p) REVERT: D 324 THR cc_start: 0.8799 (p) cc_final: 0.8592 (t) REVERT: E 234 SER cc_start: 0.8397 (m) cc_final: 0.8038 (p) REVERT: E 314 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.7945 (tp40) outliers start: 21 outliers final: 10 residues processed: 207 average time/residue: 1.4951 time to fit residues: 336.6611 Evaluate side-chains 207 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 194 time to evaluate : 1.826 ------------------------------------------------------------------------------- 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 96 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 324 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 156 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 139 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 246 GLN A 41 GLN B 41 GLN D 225 ASN D 246 GLN E 353 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.121595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.103857 restraints weight = 13644.753| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 0.96 r_work: 0.3034 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2082 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= 0.163 Angle : 0.635 7.605 20170 Z= 0.310 Chirality : 0.048 0.179 2240 Planarity : 0.004 0.033 2570 Dihedral : 11.889 175.018 2060 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.16 % Allowed : 11.00 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.20), residues: 1800 helix: 0.45 (0.19), residues: 790 sheet: 0.02 (0.26), residues: 335 loop : 1.94 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 79 HIS 0.005 0.001 HIS D 161 PHE 0.013 0.002 PHE B 262 TYR 0.011 0.001 TYR B 143 ARG 0.005 0.000 ARG D 372 Details of bonding type rmsd hydrogen bonds : bond 0.04302 ( 728) hydrogen bonds : angle 4.90575 ( 1848) covalent geometry : bond 0.00363 (14860) covalent geometry : angle 0.63527 (20170) *********************** 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 209 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 1.654 Fit side-chains REVERT: C 118 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8261 (mppt) REVERT: C 128 ASN cc_start: 0.8478 (m110) cc_final: 0.8199 (m-40) REVERT: B 99 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: B 100 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7565 (pm20) REVERT: B 117 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8184 (mt-10) REVERT: B 225 ASN cc_start: 0.8337 (m110) cc_final: 0.8123 (m-40) REVERT: D 234 SER cc_start: 0.7855 (m) cc_final: 0.7601 (p) REVERT: D 324 THR cc_start: 0.8803 (p) cc_final: 0.8588 (t) REVERT: E 234 SER cc_start: 0.8417 (m) cc_final: 0.8064 (p) REVERT: E 314 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.7949 (tp40) outliers start: 18 outliers final: 12 residues processed: 201 average time/residue: 1.6060 time to fit residues: 354.5822 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 : 1.658 ------------------------------------------------------------------------------- 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 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 99 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 324 THR 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 Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 94 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 32 optimal weight: 0.0370 chunk 68 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.121192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.103396 restraints weight = 13696.389| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 0.97 r_work: 0.3026 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14860 Z= 0.180 Angle : 0.654 7.746 20170 Z= 0.321 Chirality : 0.048 0.181 2240 Planarity : 0.004 0.033 2570 Dihedral : 11.958 175.595 2060 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.22 % Allowed : 11.00 % Favored : 87.78 % 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: 1.06 (0.20), residues: 1800 helix: 0.43 (0.19), residues: 790 sheet: -0.03 (0.26), residues: 325 loop : 1.83 (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 D 161 PHE 0.014 0.002 PHE B 262 TYR 0.011 0.001 TYR B 143 ARG 0.005 0.001 ARG D 372 Details of bonding type rmsd hydrogen bonds : bond 0.04511 ( 728) hydrogen bonds : angle 4.97983 ( 1848) covalent geometry : bond 0.00403 (14860) covalent geometry : angle 0.65439 (20170) ********************** 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 210 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 1.771 Fit side-chains REVERT: C 118 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8238 (mppt) REVERT: C 128 ASN cc_start: 0.8494 (m110) cc_final: 0.8210 (m-40) REVERT: B 99 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: B 100 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7561 (pm20) REVERT: B 117 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8177 (mt-10) REVERT: B 225 ASN cc_start: 0.8342 (m110) cc_final: 0.8116 (m-40) REVERT: D 234 SER cc_start: 0.7865 (m) cc_final: 0.7613 (p) REVERT: D 324 THR cc_start: 0.8812 (p) cc_final: 0.8593 (t) REVERT: E 234 SER cc_start: 0.8420 (m) cc_final: 0.8065 (p) REVERT: E 314 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.7956 (tp40) outliers start: 19 outliers final: 12 residues processed: 201 average time/residue: 1.5643 time to fit residues: 341.8928 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 : 1.645 ------------------------------------------------------------------------------- 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 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 99 GLU 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 Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 106 optimal weight: 0.0870 chunk 28 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- 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 E 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.122557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.104935 restraints weight = 13719.919| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 0.96 r_work: 0.3051 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14860 Z= 0.133 Angle : 0.610 7.481 20170 Z= 0.295 Chirality : 0.046 0.177 2240 Planarity : 0.003 0.033 2570 Dihedral : 11.771 177.025 2060 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.03 % Allowed : 11.13 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.20), residues: 1800 helix: 0.59 (0.19), residues: 775 sheet: 0.04 (0.27), residues: 325 loop : 1.99 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 340 HIS 0.005 0.001 HIS D 161 PHE 0.010 0.001 PHE B 262 TYR 0.011 0.001 TYR B 143 ARG 0.005 0.000 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 728) hydrogen bonds : angle 4.79183 ( 1848) covalent geometry : bond 0.00289 (14860) covalent geometry : angle 0.60985 (20170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15134.55 seconds wall clock time: 265 minutes 1.20 seconds (15901.20 seconds total)