Starting phenix.real_space_refine on Fri Jun 13 16:42:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a2t_15106/06_2025/8a2t_15106.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a2t_15106/06_2025/8a2t_15106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a2t_15106/06_2025/8a2t_15106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a2t_15106/06_2025/8a2t_15106.map" model { file = "/net/cci-nas-00/data/ceres_data/8a2t_15106/06_2025/8a2t_15106.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a2t_15106/06_2025/8a2t_15106.cif" } resolution = 2.24 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= 0.007 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 P 10 5.49 5 Mg 5 5.21 5 S 100 5.16 5 C 9145 2.51 5 N 2445 2.21 5 O 3341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 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: 15046 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2870 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 130 Classifications: {'water': 130} Link IDs: {None: 129} Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "B" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Chain: "D" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "E" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 88 Classifications: {'water': 88} Link IDs: {None: 87} Restraints were copied for chains: C, B, E, D Time building chain proxies: 7.81, per 1000 atoms: 0.52 Number of scatterers: 15046 At special positions: 0 Unit cell: (96.605, 91.045, 193.21, 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) S 100 16.00 P 10 15.00 Mg 5 11.99 O 3341 8.00 N 2445 7.00 C 9145 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: 4.21 Conformation dependent library (CDL) restraints added in 1.8 seconds 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3400 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 30 sheets defined 52.7% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 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 removed outlier: 3.631A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.008A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.550A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.797A 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 305 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: 3.752A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 371 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 removed outlier: 3.629A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.009A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.550A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.796A 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 305 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: 3.751A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 371 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 removed outlier: 3.631A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.008A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.550A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.797A 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 305 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: 3.752A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 371 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 removed outlier: 3.630A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.009A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.550A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.797A 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 305 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: 3.752A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 371 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 removed outlier: 3.630A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.010A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 removed outlier: 3.549A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.797A 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 305 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: 3.751A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 371 Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.566A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.370A 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: 4.074A 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: 4.074A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 6.229A 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: 6.228A 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: 3.911A 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: 6.566A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.370A 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: 6.566A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.371A 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: 6.228A 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: 4.180A 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: 6.566A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.370A 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: 6.228A 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: 6.567A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.371A 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: 6.228A 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. 1878 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.09 Time building geometry restraints manager: 4.92 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: 4701 1.34 - 1.46: 2868 1.46 - 1.57: 7046 1.57 - 1.69: 15 1.69 - 1.81: 175 Bond restraints: 14805 Sorted by residual: bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.79e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.79e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.70e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.67e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.53e+00 ... (remaining 14800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 19642 1.46 - 2.91: 312 2.91 - 4.37: 98 4.37 - 5.83: 28 5.83 - 7.28: 10 Bond angle restraints: 20090 Sorted by residual: angle pdb=" N VAL B 43 " pdb=" CA VAL B 43 " pdb=" C VAL B 43 " ideal model delta sigma weight residual 113.71 110.30 3.41 9.50e-01 1.11e+00 1.29e+01 angle pdb=" N VAL D 43 " pdb=" CA VAL D 43 " pdb=" C VAL D 43 " ideal model delta sigma weight residual 113.71 110.31 3.40 9.50e-01 1.11e+00 1.28e+01 angle pdb=" N VAL A 43 " pdb=" CA VAL A 43 " pdb=" C VAL A 43 " ideal model delta sigma weight residual 113.71 110.36 3.35 9.50e-01 1.11e+00 1.24e+01 angle pdb=" N VAL E 43 " pdb=" CA VAL E 43 " pdb=" C VAL E 43 " ideal model delta sigma weight residual 113.71 110.36 3.35 9.50e-01 1.11e+00 1.24e+01 angle pdb=" N VAL C 43 " pdb=" CA VAL C 43 " pdb=" C VAL C 43 " ideal model delta sigma weight residual 113.71 110.37 3.34 9.50e-01 1.11e+00 1.24e+01 ... (remaining 20085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.63: 8790 33.63 - 67.27: 80 67.27 - 100.90: 30 100.90 - 134.54: 5 134.54 - 168.17: 5 Dihedral angle restraints: 8910 sinusoidal: 3610 harmonic: 5300 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 -60.00 108.18 -168.17 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 108.16 -168.16 1 2.00e+01 2.50e-03 4.75e+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 -60.00 108.14 -168.14 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 8907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1239 0.031 - 0.062: 696 0.062 - 0.094: 176 0.094 - 0.125: 113 0.125 - 0.156: 6 Chirality restraints: 2230 Sorted by residual: 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 -2.67 0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" C3' ADP E 401 " pdb=" C2' ADP E 401 " pdb=" C4' ADP E 401 " pdb=" O3' ADP E 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.79e-01 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 5.77e-01 ... (remaining 2227 not shown) Planarity restraints: 2565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 163 " -0.017 5.00e-02 4.00e+02 2.60e-02 1.08e+00 pdb=" N PRO C 164 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 163 " -0.017 5.00e-02 4.00e+02 2.59e-02 1.08e+00 pdb=" N PRO E 164 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO E 164 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 164 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 163 " -0.017 5.00e-02 4.00e+02 2.59e-02 1.08e+00 pdb=" N PRO A 164 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " -0.014 5.00e-02 4.00e+02 ... (remaining 2562 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 133 2.48 - 3.09: 10361 3.09 - 3.69: 24256 3.69 - 4.30: 39521 4.30 - 4.90: 61090 Nonbonded interactions: 135361 Sorted by model distance: nonbonded pdb="MG MG E 402 " pdb=" O HOH E 522 " model vdw 1.880 2.170 nonbonded pdb="MG MG B 402 " pdb=" O HOH B 528 " model vdw 1.891 2.170 nonbonded pdb="MG MG C 402 " pdb=" O HOH C 544 " model vdw 1.892 2.170 nonbonded pdb="MG MG D 402 " pdb=" O HOH D 536 " model vdw 1.925 2.170 nonbonded pdb="MG MG C 402 " pdb=" O HOH C 545 " model vdw 1.928 2.170 ... (remaining 135356 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: 0.12 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: 4.360 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: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 37.880 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:14.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 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 : 0.004 0.056 14805 Z= 0.174 Angle : 0.564 7.282 20090 Z= 0.286 Chirality : 0.044 0.156 2230 Planarity : 0.004 0.026 2565 Dihedral : 13.196 168.175 5510 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.32 % Allowed : 4.19 % Favored : 95.48 % 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: -1.62 (0.19), residues: 1795 helix: -2.37 (0.14), residues: 785 sheet: -1.01 (0.25), residues: 305 loop : 0.95 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 340 HIS 0.003 0.001 HIS B 161 PHE 0.007 0.001 PHE E 262 TYR 0.009 0.001 TYR E 143 ARG 0.003 0.001 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.22866 ( 728) hydrogen bonds : angle 8.01184 ( 1878) covalent geometry : bond 0.00387 (14805) covalent geometry : angle 0.56422 (20090) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 246 time to evaluate : 1.677 Fit side-chains revert: symmetry clash REVERT: C 41 GLN cc_start: 0.7078 (mp10) cc_final: 0.6659 (mp10) REVERT: B 41 GLN cc_start: 0.6963 (mp10) cc_final: 0.6663 (mp10) REVERT: B 72 GLU cc_start: 0.7419 (tp30) cc_final: 0.7020 (tp30) REVERT: B 121 GLN cc_start: 0.8126 (tt0) cc_final: 0.7901 (tt0) REVERT: B 123 MET cc_start: 0.8970 (mmt) cc_final: 0.8715 (mmp) REVERT: D 25 ASP cc_start: 0.7743 (p0) cc_final: 0.7349 (m-30) REVERT: D 41 GLN cc_start: 0.6559 (mp10) cc_final: 0.6338 (mp10) REVERT: E 41 GLN cc_start: 0.6894 (mp10) cc_final: 0.6554 (mp10) outliers start: 5 outliers final: 1 residues processed: 250 average time/residue: 1.5951 time to fit residues: 432.2689 Evaluate side-chains 188 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 178 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.0050 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 0.0170 chunk 46 optimal weight: 6.9990 chunk 92 optimal weight: 0.4980 chunk 72 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 overall best weight: 0.7034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 GLN A 225 ASN A 246 GLN A 354 GLN B 354 GLN D 246 GLN D 353 GLN E 40 HIS E 88 HIS E 353 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.097505 restraints weight = 15641.146| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.22 r_work: 0.3017 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14805 Z= 0.104 Angle : 0.561 7.660 20090 Z= 0.269 Chirality : 0.043 0.184 2230 Planarity : 0.004 0.032 2565 Dihedral : 11.769 169.650 2057 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.48 % Allowed : 7.23 % Favored : 91.29 % 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: 0.48 (0.20), residues: 1795 helix: -0.30 (0.17), residues: 770 sheet: -0.40 (0.24), residues: 345 loop : 1.95 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 79 HIS 0.002 0.001 HIS E 88 PHE 0.008 0.001 PHE D 262 TYR 0.011 0.001 TYR E 143 ARG 0.002 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 728) hydrogen bonds : angle 5.13615 ( 1878) covalent geometry : bond 0.00218 (14805) covalent geometry : angle 0.56082 (20090) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 1.847 Fit side-chains REVERT: C 41 GLN cc_start: 0.7318 (mp10) cc_final: 0.7004 (mp10) REVERT: C 211 ASP cc_start: 0.8539 (t70) cc_final: 0.8300 (t70) REVERT: C 328 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8595 (tttt) REVERT: A 57 GLU cc_start: 0.8051 (tt0) cc_final: 0.7816 (pt0) REVERT: B 41 GLN cc_start: 0.7305 (mp10) cc_final: 0.6953 (mp10) REVERT: B 121 GLN cc_start: 0.8543 (tt0) cc_final: 0.8312 (tt0) REVERT: B 354 GLN cc_start: 0.8297 (pt0) cc_final: 0.7990 (pm20) REVERT: D 25 ASP cc_start: 0.8263 (p0) cc_final: 0.7657 (m-30) REVERT: D 95 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7872 (mtp180) REVERT: D 334 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7224 (pp20) REVERT: E 41 GLN cc_start: 0.7336 (mp10) cc_final: 0.7067 (mp10) outliers start: 23 outliers final: 8 residues processed: 205 average time/residue: 1.6810 time to fit residues: 372.8077 Evaluate side-chains 189 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 109 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 49 optimal weight: 0.3980 chunk 102 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 167 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 HIS C 353 GLN A 59 GLN A 225 ASN A 354 GLN D 40 HIS E 88 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.113378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.094366 restraints weight = 15615.033| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.21 r_work: 0.2964 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14805 Z= 0.185 Angle : 0.624 8.775 20090 Z= 0.307 Chirality : 0.047 0.210 2230 Planarity : 0.004 0.039 2565 Dihedral : 12.060 171.150 2055 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.55 % Allowed : 7.61 % Favored : 90.84 % 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: 1795 helix: 0.39 (0.18), residues: 775 sheet: -0.31 (0.27), residues: 315 loop : 1.91 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 340 HIS 0.003 0.001 HIS D 161 PHE 0.015 0.002 PHE D 262 TYR 0.013 0.001 TYR E 143 ARG 0.004 0.001 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.04434 ( 728) hydrogen bonds : angle 5.00482 ( 1878) covalent geometry : bond 0.00422 (14805) covalent geometry : angle 0.62390 (20090) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 1.741 Fit side-chains revert: symmetry clash REVERT: C 41 GLN cc_start: 0.7340 (mp10) cc_final: 0.7033 (mp10) REVERT: C 328 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8592 (tttt) REVERT: A 57 GLU cc_start: 0.8317 (tt0) cc_final: 0.7923 (pt0) REVERT: A 64 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.8638 (pp) REVERT: B 41 GLN cc_start: 0.7309 (mp10) cc_final: 0.7033 (mp10) REVERT: B 72 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7482 (mm-30) REVERT: B 121 GLN cc_start: 0.8473 (tt0) cc_final: 0.8270 (tt0) REVERT: B 299 MET cc_start: 0.8760 (mtt) cc_final: 0.8523 (mtp) REVERT: B 354 GLN cc_start: 0.8370 (pt0) cc_final: 0.8115 (pm20) REVERT: D 25 ASP cc_start: 0.8341 (p0) cc_final: 0.7778 (m-30) REVERT: D 95 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7980 (mtp180) REVERT: E 41 GLN cc_start: 0.7373 (mp10) cc_final: 0.7017 (mp10) REVERT: E 50 LYS cc_start: 0.7864 (mtmm) cc_final: 0.7611 (mtpt) REVERT: E 314 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8138 (tt0) outliers start: 24 outliers final: 6 residues processed: 203 average time/residue: 1.6225 time to fit residues: 356.7171 Evaluate side-chains 186 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 45 optimal weight: 6.9990 chunk 178 optimal weight: 7.9990 chunk 167 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 176 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.114259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.095527 restraints weight = 15597.377| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.20 r_work: 0.2990 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14805 Z= 0.153 Angle : 0.595 8.246 20090 Z= 0.289 Chirality : 0.045 0.204 2230 Planarity : 0.004 0.040 2565 Dihedral : 11.976 172.571 2055 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.35 % Allowed : 8.45 % Favored : 90.19 % 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: 1.34 (0.20), residues: 1795 helix: 0.75 (0.19), residues: 775 sheet: -0.24 (0.27), residues: 315 loop : 2.00 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 79 HIS 0.003 0.001 HIS A 161 PHE 0.013 0.001 PHE D 262 TYR 0.010 0.001 TYR E 143 ARG 0.003 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 728) hydrogen bonds : angle 4.80894 ( 1878) covalent geometry : bond 0.00345 (14805) covalent geometry : angle 0.59467 (20090) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 1.821 Fit side-chains revert: symmetry clash REVERT: C 41 GLN cc_start: 0.7378 (mp10) cc_final: 0.7120 (mp10) REVERT: C 64 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.8916 (pp) REVERT: C 328 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8592 (tttt) REVERT: A 41 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7135 (mp10) REVERT: A 57 GLU cc_start: 0.8330 (tt0) cc_final: 0.7933 (pt0) REVERT: A 64 ILE cc_start: 0.9363 (OUTLIER) cc_final: 0.8670 (pp) REVERT: B 41 GLN cc_start: 0.7331 (mp10) cc_final: 0.7083 (mp10) REVERT: B 72 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7489 (mm-30) REVERT: B 299 MET cc_start: 0.8760 (mtt) cc_final: 0.8537 (mtp) REVERT: B 354 GLN cc_start: 0.8358 (pt0) cc_final: 0.8082 (pm20) REVERT: D 25 ASP cc_start: 0.8323 (p0) cc_final: 0.7807 (m-30) REVERT: D 64 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8869 (pp) REVERT: D 95 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7976 (mtp180) REVERT: E 41 GLN cc_start: 0.7398 (mp10) cc_final: 0.7020 (mp10) REVERT: E 314 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8153 (tt0) outliers start: 21 outliers final: 6 residues processed: 196 average time/residue: 1.5893 time to fit residues: 338.2647 Evaluate side-chains 185 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 77 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN D 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.113852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.095049 restraints weight = 15762.118| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.21 r_work: 0.2981 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14805 Z= 0.161 Angle : 0.602 8.292 20090 Z= 0.293 Chirality : 0.046 0.208 2230 Planarity : 0.004 0.039 2565 Dihedral : 11.999 173.021 2055 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.35 % Allowed : 8.58 % Favored : 90.06 % 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: 1.44 (0.20), residues: 1795 helix: 0.88 (0.19), residues: 775 sheet: -0.25 (0.27), residues: 315 loop : 2.04 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 340 HIS 0.003 0.001 HIS A 161 PHE 0.013 0.001 PHE D 262 TYR 0.010 0.001 TYR E 143 ARG 0.003 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.03948 ( 728) hydrogen bonds : angle 4.78446 ( 1878) covalent geometry : bond 0.00365 (14805) covalent geometry : angle 0.60157 (20090) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 1.712 Fit side-chains revert: symmetry clash REVERT: C 41 GLN cc_start: 0.7418 (mp10) cc_final: 0.7163 (mp10) REVERT: C 64 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8919 (pp) REVERT: C 121 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.8080 (tt0) REVERT: C 328 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8586 (tttt) REVERT: A 41 GLN cc_start: 0.7588 (mm-40) cc_final: 0.7158 (mp10) REVERT: A 57 GLU cc_start: 0.8348 (tt0) cc_final: 0.7903 (pt0) REVERT: A 64 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.8678 (pp) REVERT: A 326 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8374 (mmtt) REVERT: B 41 GLN cc_start: 0.7342 (mp10) cc_final: 0.7031 (mp10) REVERT: B 72 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7489 (mm-30) REVERT: B 121 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8299 (tt0) REVERT: B 299 MET cc_start: 0.8743 (mtt) cc_final: 0.8532 (mtp) REVERT: B 354 GLN cc_start: 0.8401 (pt0) cc_final: 0.8133 (pm20) REVERT: D 25 ASP cc_start: 0.8312 (p0) cc_final: 0.7788 (m-30) REVERT: D 64 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8869 (pp) REVERT: D 95 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7992 (mtp180) REVERT: E 41 GLN cc_start: 0.7363 (mp10) cc_final: 0.6974 (mp10) REVERT: E 57 GLU cc_start: 0.8132 (pt0) cc_final: 0.7876 (pt0) REVERT: E 314 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8131 (tt0) outliers start: 21 outliers final: 9 residues processed: 192 average time/residue: 1.5236 time to fit residues: 318.1926 Evaluate side-chains 193 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 78 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 175 optimal weight: 0.3980 chunk 119 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN D 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.097641 restraints weight = 15702.126| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.21 r_work: 0.3026 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 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 : 0.002 0.025 14805 Z= 0.102 Angle : 0.550 7.426 20090 Z= 0.262 Chirality : 0.043 0.183 2230 Planarity : 0.003 0.038 2565 Dihedral : 11.659 178.641 2055 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.10 % Allowed : 9.16 % Favored : 89.74 % 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: 1.72 (0.20), residues: 1795 helix: 1.12 (0.19), residues: 775 sheet: -0.09 (0.25), residues: 345 loop : 2.27 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 79 HIS 0.003 0.001 HIS E 161 PHE 0.008 0.001 PHE D 262 TYR 0.008 0.001 TYR B 143 ARG 0.002 0.000 ARG A 28 Details of bonding type rmsd hydrogen bonds : bond 0.03106 ( 728) hydrogen bonds : angle 4.54286 ( 1878) covalent geometry : bond 0.00218 (14805) covalent geometry : angle 0.55037 (20090) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 1.812 Fit side-chains REVERT: C 41 GLN cc_start: 0.7420 (mp10) cc_final: 0.7190 (mp10) REVERT: C 64 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.8853 (pp) REVERT: C 211 ASP cc_start: 0.8597 (t70) cc_final: 0.8310 (t70) REVERT: C 328 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8572 (tttt) REVERT: A 41 GLN cc_start: 0.7600 (mm-40) cc_final: 0.7210 (mp10) REVERT: A 57 GLU cc_start: 0.8307 (tt0) cc_final: 0.7921 (pt0) REVERT: A 64 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.8617 (pp) REVERT: B 41 GLN cc_start: 0.7362 (mp10) cc_final: 0.7062 (mp10) REVERT: B 354 GLN cc_start: 0.8348 (pt0) cc_final: 0.8082 (pm20) REVERT: D 25 ASP cc_start: 0.8213 (p0) cc_final: 0.7726 (m-30) REVERT: D 95 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7967 (mtp180) REVERT: E 41 GLN cc_start: 0.7370 (mp10) cc_final: 0.7029 (mp10) REVERT: E 314 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8192 (tt0) outliers start: 17 outliers final: 6 residues processed: 196 average time/residue: 1.8982 time to fit residues: 404.0436 Evaluate side-chains 183 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 172 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 95 ARG 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 32 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 177 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN D 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.113063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.094234 restraints weight = 15758.239| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.21 r_work: 0.2968 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 14805 Z= 0.203 Angle : 0.632 8.547 20090 Z= 0.311 Chirality : 0.048 0.209 2230 Planarity : 0.004 0.038 2565 Dihedral : 12.066 173.942 2055 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.48 % Allowed : 9.16 % Favored : 89.35 % 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: 1.38 (0.20), residues: 1795 helix: 0.87 (0.19), residues: 790 sheet: -0.21 (0.27), residues: 315 loop : 1.92 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 340 HIS 0.004 0.001 HIS A 161 PHE 0.016 0.002 PHE D 262 TYR 0.011 0.001 TYR E 143 ARG 0.004 0.001 ARG E 210 Details of bonding type rmsd hydrogen bonds : bond 0.04301 ( 728) hydrogen bonds : angle 4.81253 ( 1878) covalent geometry : bond 0.00469 (14805) covalent geometry : angle 0.63205 (20090) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 1.681 Fit side-chains revert: symmetry clash REVERT: C 41 GLN cc_start: 0.7382 (mp10) cc_final: 0.7138 (mp10) REVERT: C 64 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.8920 (pp) REVERT: C 121 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8127 (tt0) REVERT: C 328 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8566 (tttt) REVERT: A 41 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7222 (mp10) REVERT: A 57 GLU cc_start: 0.8350 (tt0) cc_final: 0.7910 (pt0) REVERT: A 64 ILE cc_start: 0.9371 (OUTLIER) cc_final: 0.8697 (pp) REVERT: A 326 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8374 (mmtt) REVERT: B 41 GLN cc_start: 0.7277 (mp10) cc_final: 0.7017 (mp10) REVERT: B 121 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8290 (tt0) REVERT: B 354 GLN cc_start: 0.8392 (pt0) cc_final: 0.8134 (pm20) REVERT: D 25 ASP cc_start: 0.8318 (p0) cc_final: 0.7795 (m-30) REVERT: D 95 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7997 (mtp180) REVERT: E 41 GLN cc_start: 0.7391 (mp10) cc_final: 0.7005 (mp10) REVERT: E 314 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8135 (tt0) outliers start: 23 outliers final: 11 residues processed: 188 average time/residue: 1.5860 time to fit residues: 323.9012 Evaluate side-chains 188 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 178 LEU 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 145 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN D 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.114178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.095469 restraints weight = 15667.430| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.21 r_work: 0.2989 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14805 Z= 0.149 Angle : 0.593 8.068 20090 Z= 0.287 Chirality : 0.045 0.202 2230 Planarity : 0.004 0.039 2565 Dihedral : 11.937 174.547 2055 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.03 % Allowed : 9.74 % Favored : 89.23 % 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: 1.64 (0.20), residues: 1795 helix: 1.02 (0.19), residues: 775 sheet: -0.07 (0.26), residues: 345 loop : 2.23 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 340 HIS 0.003 0.001 HIS A 161 PHE 0.012 0.001 PHE D 262 TYR 0.009 0.001 TYR E 143 ARG 0.002 0.000 ARG A 28 Details of bonding type rmsd hydrogen bonds : bond 0.03745 ( 728) hydrogen bonds : angle 4.68923 ( 1878) covalent geometry : bond 0.00335 (14805) covalent geometry : angle 0.59273 (20090) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 2.121 Fit side-chains revert: symmetry clash REVERT: C 41 GLN cc_start: 0.7378 (mp10) cc_final: 0.7140 (mp10) REVERT: C 64 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.8912 (pp) REVERT: C 121 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.8108 (tt0) REVERT: C 328 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8573 (tttt) REVERT: A 41 GLN cc_start: 0.7604 (mm-40) cc_final: 0.7218 (mp10) REVERT: A 57 GLU cc_start: 0.8341 (tt0) cc_final: 0.7935 (pt0) REVERT: A 64 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.8671 (pp) REVERT: B 41 GLN cc_start: 0.7235 (mp10) cc_final: 0.6979 (mp10) REVERT: B 354 GLN cc_start: 0.8350 (pt0) cc_final: 0.8066 (pm20) REVERT: D 25 ASP cc_start: 0.8291 (p0) cc_final: 0.7771 (m-30) REVERT: D 95 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8029 (mtp180) REVERT: E 41 GLN cc_start: 0.7379 (mp10) cc_final: 0.6989 (mp10) REVERT: E 314 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8143 (tt0) outliers start: 16 outliers final: 8 residues processed: 186 average time/residue: 1.7310 time to fit residues: 350.2384 Evaluate side-chains 185 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 2 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN D 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.115194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.096603 restraints weight = 15616.934| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.20 r_work: 0.3008 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14805 Z= 0.121 Angle : 0.570 7.699 20090 Z= 0.273 Chirality : 0.044 0.187 2230 Planarity : 0.003 0.039 2565 Dihedral : 11.786 178.572 2055 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.16 % Allowed : 9.61 % Favored : 89.23 % 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: 1.76 (0.20), residues: 1795 helix: 1.12 (0.19), residues: 775 sheet: -0.04 (0.26), residues: 345 loop : 2.30 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 79 HIS 0.003 0.001 HIS E 161 PHE 0.010 0.001 PHE D 262 TYR 0.008 0.001 TYR E 143 ARG 0.002 0.000 ARG A 28 Details of bonding type rmsd hydrogen bonds : bond 0.03373 ( 728) hydrogen bonds : angle 4.57857 ( 1878) covalent geometry : bond 0.00267 (14805) covalent geometry : angle 0.56966 (20090) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 1.730 Fit side-chains REVERT: C 41 GLN cc_start: 0.7409 (mp10) cc_final: 0.7178 (mp10) REVERT: C 64 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.8865 (pp) REVERT: C 121 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8087 (tt0) REVERT: C 211 ASP cc_start: 0.8632 (t70) cc_final: 0.8341 (t70) REVERT: C 328 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8599 (tttt) REVERT: A 41 GLN cc_start: 0.7593 (mm-40) cc_final: 0.7227 (mp10) REVERT: A 57 GLU cc_start: 0.8318 (tt0) cc_final: 0.7923 (pt0) REVERT: A 64 ILE cc_start: 0.9363 (OUTLIER) cc_final: 0.8661 (pp) REVERT: B 41 GLN cc_start: 0.7230 (mp10) cc_final: 0.6978 (mp10) REVERT: B 354 GLN cc_start: 0.8329 (pt0) cc_final: 0.8051 (pm20) REVERT: D 25 ASP cc_start: 0.8275 (p0) cc_final: 0.7767 (m-30) REVERT: D 64 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8793 (pp) REVERT: D 95 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7976 (mtp180) REVERT: E 41 GLN cc_start: 0.7432 (mp10) cc_final: 0.7064 (mp10) REVERT: E 314 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8210 (tt0) outliers start: 18 outliers final: 9 residues processed: 186 average time/residue: 1.6866 time to fit residues: 340.4847 Evaluate side-chains 189 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 118 LYS 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 154 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN D 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.113521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.094766 restraints weight = 15721.084| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.21 r_work: 0.2977 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14805 Z= 0.177 Angle : 0.618 8.317 20090 Z= 0.302 Chirality : 0.046 0.203 2230 Planarity : 0.004 0.038 2565 Dihedral : 11.982 176.148 2055 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.10 % Allowed : 9.94 % Favored : 88.97 % 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: 1.60 (0.20), residues: 1795 helix: 1.00 (0.19), residues: 775 sheet: -0.18 (0.28), residues: 315 loop : 2.13 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 340 HIS 0.003 0.001 HIS A 161 PHE 0.014 0.002 PHE D 262 TYR 0.010 0.001 TYR E 143 ARG 0.007 0.000 ARG A 28 Details of bonding type rmsd hydrogen bonds : bond 0.04048 ( 728) hydrogen bonds : angle 4.74606 ( 1878) covalent geometry : bond 0.00406 (14805) covalent geometry : angle 0.61778 (20090) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 1.750 Fit side-chains revert: symmetry clash REVERT: C 41 GLN cc_start: 0.7384 (mp10) cc_final: 0.7143 (mp10) REVERT: C 64 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.8920 (pp) REVERT: C 121 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.8101 (tt0) REVERT: C 328 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8569 (tttt) REVERT: A 41 GLN cc_start: 0.7599 (mm-40) cc_final: 0.7222 (mp10) REVERT: A 57 GLU cc_start: 0.8348 (tt0) cc_final: 0.7925 (pt0) REVERT: A 64 ILE cc_start: 0.9371 (OUTLIER) cc_final: 0.8684 (pp) REVERT: A 326 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8371 (mmtt) REVERT: B 41 GLN cc_start: 0.7224 (mp10) cc_final: 0.6959 (mp10) REVERT: B 354 GLN cc_start: 0.8383 (pt0) cc_final: 0.8097 (pm20) REVERT: D 25 ASP cc_start: 0.8311 (p0) cc_final: 0.7826 (m-30) REVERT: D 64 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8786 (pp) REVERT: D 95 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8020 (mtp180) REVERT: E 41 GLN cc_start: 0.7397 (mp10) cc_final: 0.7011 (mp10) REVERT: E 314 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8177 (tt0) outliers start: 17 outliers final: 8 residues processed: 182 average time/residue: 1.6518 time to fit residues: 327.1920 Evaluate side-chains 186 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 95 ARG 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 112 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 164 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN D 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.113892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.095187 restraints weight = 15740.654| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.21 r_work: 0.2984 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14805 Z= 0.161 Angle : 0.604 8.203 20090 Z= 0.294 Chirality : 0.046 0.202 2230 Planarity : 0.004 0.039 2565 Dihedral : 11.953 175.263 2055 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.03 % Allowed : 9.87 % Favored : 89.10 % 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: 1.61 (0.20), residues: 1795 helix: 1.03 (0.19), residues: 775 sheet: -0.20 (0.27), residues: 315 loop : 2.12 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 340 HIS 0.003 0.001 HIS A 161 PHE 0.012 0.001 PHE D 262 TYR 0.009 0.001 TYR E 143 ARG 0.008 0.000 ARG A 28 Details of bonding type rmsd hydrogen bonds : bond 0.03858 ( 728) hydrogen bonds : angle 4.69883 ( 1878) covalent geometry : bond 0.00365 (14805) covalent geometry : angle 0.60431 (20090) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14122.62 seconds wall clock time: 246 minutes 22.01 seconds (14782.01 seconds total)