Starting phenix.real_space_refine on Sat Sep 12 09:40:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5ooc_3836/09_2026/5ooc_3836.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ooc_3836/09_2026/5ooc_3836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5ooc_3836/09_2026/5ooc_3836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ooc_3836/09_2026/5ooc_3836.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5ooc_3836/09_2026/5ooc_3836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ooc_3836/09_2026/5ooc_3836.map" restraint_files = "/net/cci-nas-00/data/ceres_data/5ooc_3836/09_2026/5ooc_3836.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5ooc_3836/09_2026/5ooc_3836.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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 105 5.16 5 C 9425 2.51 5 N 2495 2.21 5 O 2845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14885 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: "E" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 126 Unusual residues: {' MG': 1, '9ZK': 2, 'ADP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" 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} Time building chain proxies: 3.42, per 1000 atoms: 0.23 Number of scatterers: 14885 At special positions: 0 Unit cell: (100.32, 85.5, 190.38, 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 105 16.00 P 10 15.00 Mg 5 11.99 O 2845 8.00 N 2495 7.00 C 9425 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: 1.33 Conformation dependent library (CDL) restraints added in 745.0 milliseconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 25 sheets defined 52.3% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... 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: 4.135A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 181 through 194 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 230 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 295 removed outlier: 4.485A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) 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 349 Processing helix chain 'A' and resid 350 through 356 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 372 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: 4.134A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 171 through 175 Processing helix chain 'B' and resid 181 through 194 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 230 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 295 removed outlier: 4.485A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) 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 349 Processing helix chain 'B' and resid 350 through 356 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 372 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: 4.134A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 181 through 194 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 230 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 295 removed outlier: 4.484A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) 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 349 Processing helix chain 'C' and resid 350 through 356 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 372 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: 4.134A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 171 through 175 Processing helix chain 'D' and resid 181 through 194 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 230 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 295 removed outlier: 4.485A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) 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 349 Processing helix chain 'D' and resid 350 through 356 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 372 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: 4.134A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 181 through 194 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 230 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 295 removed outlier: 4.485A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) 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 349 Processing helix chain 'E' and resid 350 through 356 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 372 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.781A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.781A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 178 Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.780A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB4, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'C' and resid 176 through 178 Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.781A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC1, first strand: chain 'D' and resid 176 through 178 Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC3, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.782A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC5, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AC6, first strand: chain 'E' and resid 176 through 178 Processing sheet with id=AC7, first strand: chain 'E' and resid 238 through 241 765 hydrogen bonds defined for protein. 1920 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.86 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 2455 1.28 - 1.41: 3835 1.41 - 1.54: 8721 1.54 - 1.68: 24 1.68 - 1.81: 185 Bond restraints: 15220 Sorted by residual: bond pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.58e+01 ... (remaining 15215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 18866 2.58 - 5.15: 1451 5.15 - 7.73: 253 7.73 - 10.30: 45 10.30 - 12.88: 45 Bond angle restraints: 20660 Sorted by residual: angle pdb=" C PHE A 31 " pdb=" N PRO A 32 " pdb=" CA PRO A 32 " ideal model delta sigma weight residual 119.76 127.17 -7.41 1.00e+00 1.00e+00 5.49e+01 angle pdb=" C PHE E 31 " pdb=" N PRO E 32 " pdb=" CA PRO E 32 " ideal model delta sigma weight residual 119.76 127.15 -7.39 1.00e+00 1.00e+00 5.47e+01 angle pdb=" C PHE C 31 " pdb=" N PRO C 32 " pdb=" CA PRO C 32 " ideal model delta sigma weight residual 119.76 127.14 -7.38 1.00e+00 1.00e+00 5.45e+01 angle pdb=" C PHE B 31 " pdb=" N PRO B 32 " pdb=" CA PRO B 32 " ideal model delta sigma weight residual 119.76 127.14 -7.38 1.00e+00 1.00e+00 5.45e+01 angle pdb=" C PHE D 31 " pdb=" N PRO D 32 " pdb=" CA PRO D 32 " ideal model delta sigma weight residual 119.76 127.13 -7.37 1.00e+00 1.00e+00 5.44e+01 ... (remaining 20655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.85: 8870 29.85 - 59.69: 190 59.69 - 89.54: 81 89.54 - 119.38: 69 119.38 - 149.23: 30 Dihedral angle restraints: 9240 sinusoidal: 3880 harmonic: 5360 Sorted by residual: dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 89.22 -149.23 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 89.20 -149.20 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 89.20 -149.20 1 2.00e+01 2.50e-03 4.46e+01 ... (remaining 9237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1808 0.087 - 0.174: 441 0.174 - 0.261: 26 0.261 - 0.348: 0 0.348 - 0.435: 5 Chirality restraints: 2280 Sorted by residual: chirality pdb=" C25 9ZK A 402 " pdb=" C26 9ZK A 402 " pdb=" C36 9ZK A 402 " pdb=" N23 9ZK A 402 " both_signs ideal model delta sigma weight residual False 2.15 2.58 -0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" C25 9ZK A 404 " pdb=" C26 9ZK A 404 " pdb=" C36 9ZK A 404 " pdb=" N23 9ZK A 404 " both_signs ideal model delta sigma weight residual False 2.15 2.58 -0.43 2.00e-01 2.50e+01 4.72e+00 chirality pdb=" C25 9ZK B 403 " pdb=" C26 9ZK B 403 " pdb=" C36 9ZK B 403 " pdb=" N23 9ZK B 403 " both_signs ideal model delta sigma weight residual False 2.15 2.58 -0.43 2.00e-01 2.50e+01 4.71e+00 ... (remaining 2277 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 163 " -0.097 5.00e-02 4.00e+02 1.47e-01 3.45e+01 pdb=" N PRO A 164 " 0.254 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 163 " -0.097 5.00e-02 4.00e+02 1.47e-01 3.45e+01 pdb=" N PRO B 164 " 0.254 5.00e-02 4.00e+02 pdb=" CA PRO B 164 " -0.082 5.00e-02 4.00e+02 pdb=" CD PRO B 164 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 163 " 0.097 5.00e-02 4.00e+02 1.47e-01 3.44e+01 pdb=" N PRO C 164 " -0.254 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " 0.082 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " 0.075 5.00e-02 4.00e+02 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 170 2.62 - 3.19: 14784 3.19 - 3.76: 23000 3.76 - 4.33: 34499 4.33 - 4.90: 53380 Nonbonded interactions: 125833 Sorted by model distance: nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.050 2.170 nonbonded pdb=" O2B ADP E 401 " pdb="MG MG E 402 " model vdw 2.050 2.170 nonbonded pdb=" O2B ADP A 401 " pdb="MG MG A 403 " model vdw 2.050 2.170 nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 2.051 2.170 nonbonded pdb=" O2B ADP D 401 " pdb="MG MG D 402 " model vdw 2.051 2.170 ... (remaining 125828 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 401) selection = (chain 'B' and resid 5 through 401) selection = (chain 'C' and resid 5 through 401) selection = (chain 'D' and resid 5 through 401) selection = (chain 'E' and resid 5 through 401) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.250 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: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 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 : 0.016 0.102 15220 Z= 0.957 Angle : 1.665 12.880 20660 Z= 1.009 Chirality : 0.072 0.435 2280 Planarity : 0.018 0.147 2630 Dihedral : 21.045 149.226 5810 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 2.73 % Allowed : 4.37 % Favored : 92.90 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.20), residues: 1830 helix: -1.31 (0.16), residues: 715 sheet: -0.73 (0.26), residues: 310 loop : -0.45 (0.26), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 39 TYR 0.021 0.004 TYR B 198 PHE 0.010 0.003 PHE C 90 TRP 0.021 0.004 TRP C 340 HIS 0.007 0.002 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.01576 / 0.96 (15220) covalent geometry : angle 1.66519 / 1.01 (20660) hydrogen bonds : bond 0.17395 / 11.64 ( 765) hydrogen bonds : angle 7.35694 / 5.22 ( 1920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 500 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7640 (mtm) cc_final: 0.7219 (mpp) REVERT: A 103 THR cc_start: 0.9206 (m) cc_final: 0.8897 (p) REVERT: A 154 ASP cc_start: 0.8393 (t70) cc_final: 0.8127 (t70) REVERT: A 269 MET cc_start: 0.7298 (tpp) cc_final: 0.7007 (tpt) REVERT: A 283 MET cc_start: 0.9125 (mmp) cc_final: 0.8878 (mmp) REVERT: A 286 ASP cc_start: 0.7035 (t70) cc_final: 0.6770 (m-30) REVERT: A 355 MET cc_start: 0.7554 (mmm) cc_final: 0.7148 (mmm) REVERT: B 80 ASP cc_start: 0.8525 (m-30) cc_final: 0.8295 (t0) REVERT: B 154 ASP cc_start: 0.7274 (t70) cc_final: 0.6703 (t0) REVERT: C 47 MET cc_start: 0.5942 (mmt) cc_final: 0.5665 (mmt) REVERT: C 78 ASN cc_start: 0.8532 (t0) cc_final: 0.8238 (t0) REVERT: C 82 MET cc_start: 0.9167 (tpt) cc_final: 0.8963 (tpt) REVERT: C 178 LEU cc_start: 0.8698 (mt) cc_final: 0.8479 (mp) REVERT: C 191 LYS cc_start: 0.8573 (mttt) cc_final: 0.8257 (ttmm) REVERT: C 224 GLU cc_start: 0.8133 (tp30) cc_final: 0.7932 (tm-30) REVERT: C 238 LYS cc_start: 0.8849 (tptt) cc_final: 0.8527 (ttmt) REVERT: C 296 ASN cc_start: 0.8426 (m-40) cc_final: 0.8199 (m-40) REVERT: C 336 LYS cc_start: 0.8136 (mttt) cc_final: 0.7368 (ttmt) REVERT: D 44 MET cc_start: 0.7083 (mtm) cc_final: 0.6057 (ttt) REVERT: D 128 ASN cc_start: 0.7985 (m-40) cc_final: 0.7209 (t0) REVERT: D 201 VAL cc_start: 0.9460 (m) cc_final: 0.9046 (p) REVERT: D 211 ASP cc_start: 0.8788 (t70) cc_final: 0.8299 (t0) REVERT: D 222 ASP cc_start: 0.7416 (t0) cc_final: 0.7195 (p0) REVERT: D 249 THR cc_start: 0.9206 (m) cc_final: 0.9005 (p) REVERT: D 296 ASN cc_start: 0.8373 (m-40) cc_final: 0.7825 (m-40) REVERT: E 120 THR cc_start: 0.8371 (m) cc_final: 0.8151 (p) REVERT: E 227 MET cc_start: 0.8306 (mmm) cc_final: 0.8011 (mmm) REVERT: E 244 ASP cc_start: 0.8851 (p0) cc_final: 0.8576 (p0) REVERT: E 249 THR cc_start: 0.8795 (m) cc_final: 0.8563 (p) REVERT: E 353 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8189 (mm-40) outliers start: 0 outliers final: 0 residues processed: 500 average time/residue: 0.1285 time to fit residues: 91.4690 Evaluate side-chains 243 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.121649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.107474 restraints weight = 23225.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.110518 restraints weight = 11976.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112511 restraints weight = 7467.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113870 restraints weight = 5280.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.114796 restraints weight = 4095.558| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15220 Z= 0.151 Angle : 0.759 9.442 20660 Z= 0.375 Chirality : 0.047 0.203 2280 Planarity : 0.008 0.060 2630 Dihedral : 28.853 170.179 2330 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 1.09 % Allowed : 1.69 % Favored : 97.21 % Rotamer: Outliers : 1.60 % Allowed : 8.24 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.20), residues: 1830 helix: 1.07 (0.19), residues: 695 sheet: -0.75 (0.26), residues: 290 loop : -0.07 (0.23), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 147 TYR 0.019 0.001 TYR A 166 PHE 0.007 0.001 PHE B 90 TRP 0.016 0.001 TRP A 340 HIS 0.006 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (15220) covalent geometry : angle 0.75932 / 0.38 (20660) hydrogen bonds : bond 0.04115 / 2.74 ( 765) hydrogen bonds : angle 4.99636 / 3.46 ( 1920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 339 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 THR cc_start: 0.8882 (m) cc_final: 0.8488 (p) REVERT: A 123 MET cc_start: 0.8986 (mmm) cc_final: 0.8637 (mmt) REVERT: A 154 ASP cc_start: 0.8260 (t70) cc_final: 0.7808 (t70) REVERT: A 269 MET cc_start: 0.7211 (tpp) cc_final: 0.6713 (tpt) REVERT: A 283 MET cc_start: 0.8828 (mmp) cc_final: 0.8614 (mmp) REVERT: B 78 ASN cc_start: 0.8045 (t0) cc_final: 0.7201 (t0) REVERT: B 143 TYR cc_start: 0.7855 (m-10) cc_final: 0.7654 (m-10) REVERT: B 269 MET cc_start: 0.7210 (mmm) cc_final: 0.6683 (tpp) REVERT: C 34 ILE cc_start: 0.9361 (mt) cc_final: 0.9148 (pt) REVERT: C 41 GLN cc_start: 0.7571 (tt0) cc_final: 0.7362 (tt0) REVERT: C 78 ASN cc_start: 0.8188 (t0) cc_final: 0.7898 (t0) REVERT: C 117 GLU cc_start: 0.7402 (tt0) cc_final: 0.7183 (tt0) REVERT: C 178 LEU cc_start: 0.8595 (mt) cc_final: 0.8388 (mp) REVERT: C 336 LYS cc_start: 0.7962 (mttt) cc_final: 0.7705 (mttt) REVERT: D 161 HIS cc_start: 0.8738 (p90) cc_final: 0.8355 (p-80) REVERT: D 212 ILE cc_start: 0.8937 (mt) cc_final: 0.8655 (mt) REVERT: D 336 LYS cc_start: 0.8340 (mttt) cc_final: 0.7800 (ttmt) REVERT: E 25 ASP cc_start: 0.7429 (t0) cc_final: 0.7227 (t0) REVERT: E 57 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7581 (mm-30) REVERT: E 162 ASN cc_start: 0.8161 (m-40) cc_final: 0.7943 (m-40) REVERT: E 184 ASP cc_start: 0.7910 (m-30) cc_final: 0.7668 (m-30) REVERT: E 192 ILE cc_start: 0.9251 (mm) cc_final: 0.8887 (tp) REVERT: E 206 ARG cc_start: 0.7835 (ttm-80) cc_final: 0.7627 (ttm-80) REVERT: E 246 GLN cc_start: 0.8755 (mt0) cc_final: 0.8381 (mt0) REVERT: E 249 THR cc_start: 0.8715 (m) cc_final: 0.8485 (p) REVERT: E 292 ASP cc_start: 0.7777 (m-30) cc_final: 0.7492 (m-30) REVERT: E 313 MET cc_start: 0.8413 (tpp) cc_final: 0.8211 (ttm) outliers start: 25 outliers final: 16 residues processed: 359 average time/residue: 0.1048 time to fit residues: 57.7296 Evaluate side-chains 259 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 243 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 334 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 58 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 chunk 156 optimal weight: 0.0050 chunk 85 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 overall best weight: 1.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 161 HIS ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS E 12 ASN E 115 ASN E 121 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 = 0.3299 r_free = 0.3299 target = 0.113893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.099148 restraints weight = 23875.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.102167 restraints weight = 12194.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.104206 restraints weight = 7581.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.105594 restraints weight = 5374.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.106508 restraints weight = 4171.660| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15220 Z= 0.195 Angle : 0.725 9.503 20660 Z= 0.361 Chirality : 0.047 0.231 2280 Planarity : 0.007 0.056 2630 Dihedral : 29.480 179.698 2330 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 1.09 % Allowed : 3.06 % Favored : 95.85 % Rotamer: Outliers : 3.58 % Allowed : 11.18 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.20), residues: 1830 helix: 0.79 (0.19), residues: 765 sheet: -0.65 (0.29), residues: 280 loop : 0.14 (0.24), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 28 TYR 0.018 0.001 TYR A 166 PHE 0.025 0.002 PHE A 352 TRP 0.017 0.002 TRP A 86 HIS 0.008 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (15220) covalent geometry : angle 0.72454 / 0.36 (20660) hydrogen bonds : bond 0.04379 / 2.91 ( 765) hydrogen bonds : angle 4.77325 / 3.34 ( 1920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 286 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 THR cc_start: 0.8965 (m) cc_final: 0.8481 (p) REVERT: A 154 ASP cc_start: 0.8502 (t70) cc_final: 0.8061 (t70) REVERT: A 191 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8750 (ttpp) REVERT: A 222 ASP cc_start: 0.7191 (t0) cc_final: 0.5695 (p0) REVERT: B 78 ASN cc_start: 0.8391 (t0) cc_final: 0.7660 (t0) REVERT: B 100 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7148 (tp30) REVERT: B 151 ILE cc_start: 0.8846 (mt) cc_final: 0.8591 (tt) REVERT: B 269 MET cc_start: 0.7268 (mmm) cc_final: 0.6741 (mmt) REVERT: B 294 TYR cc_start: 0.8786 (m-10) cc_final: 0.8466 (m-10) REVERT: C 47 MET cc_start: 0.6719 (tpp) cc_final: 0.6430 (tpp) REVERT: C 78 ASN cc_start: 0.8262 (t0) cc_final: 0.7455 (t0) REVERT: C 81 ASP cc_start: 0.8588 (m-30) cc_final: 0.8349 (m-30) REVERT: C 211 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8594 (m-30) REVERT: C 283 MET cc_start: 0.8337 (mmm) cc_final: 0.7693 (mmm) REVERT: C 336 LYS cc_start: 0.8073 (mttt) cc_final: 0.7653 (ttpt) REVERT: D 192 ILE cc_start: 0.8988 (tp) cc_final: 0.8781 (tp) REVERT: D 227 MET cc_start: 0.7967 (mmm) cc_final: 0.7749 (mmm) REVERT: D 336 LYS cc_start: 0.8518 (mttt) cc_final: 0.7931 (ttmt) REVERT: E 47 MET cc_start: 0.3309 (mtt) cc_final: 0.3059 (mtt) REVERT: E 68 LYS cc_start: 0.8286 (mmtt) cc_final: 0.8046 (mmmt) REVERT: E 82 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8641 (tpt) REVERT: E 162 ASN cc_start: 0.8306 (m-40) cc_final: 0.8071 (m-40) REVERT: E 292 ASP cc_start: 0.7946 (m-30) cc_final: 0.7737 (m-30) outliers start: 56 outliers final: 34 residues processed: 320 average time/residue: 0.0996 time to fit residues: 50.0048 Evaluate side-chains 269 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 232 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 334 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 30 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 172 optimal weight: 4.9990 chunk 23 optimal weight: 0.0370 chunk 39 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 49 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 ASN C 296 ASN E 115 ASN E 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.116407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.101367 restraints weight = 23697.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.104561 restraints weight = 12070.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.106696 restraints weight = 7414.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.108091 restraints weight = 5209.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.109080 restraints weight = 4026.725| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15220 Z= 0.127 Angle : 0.654 10.047 20660 Z= 0.320 Chirality : 0.044 0.194 2280 Planarity : 0.005 0.054 2630 Dihedral : 28.786 179.922 2330 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 1.09 % Allowed : 2.84 % Favored : 96.07 % Rotamer: Outliers : 3.13 % Allowed : 13.80 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.20), residues: 1830 helix: 1.06 (0.19), residues: 765 sheet: -0.63 (0.28), residues: 305 loop : 0.37 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 206 TYR 0.013 0.001 TYR A 166 PHE 0.013 0.001 PHE B 223 TRP 0.020 0.001 TRP A 86 HIS 0.005 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (15220) covalent geometry : angle 0.65351 / 0.32 (20660) hydrogen bonds : bond 0.03417 / 2.26 ( 765) hydrogen bonds : angle 4.48090 / 3.13 ( 1920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 256 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8864 (mt) cc_final: 0.8611 (mt) REVERT: A 103 THR cc_start: 0.8839 (m) cc_final: 0.8276 (p) REVERT: A 154 ASP cc_start: 0.8446 (t70) cc_final: 0.7967 (t70) REVERT: A 222 ASP cc_start: 0.6597 (t0) cc_final: 0.5999 (p0) REVERT: A 328 LYS cc_start: 0.8439 (tmtt) cc_final: 0.8238 (tmtt) REVERT: B 78 ASN cc_start: 0.8368 (t0) cc_final: 0.7664 (t0) REVERT: B 100 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7102 (tp30) REVERT: B 161 HIS cc_start: 0.8813 (p-80) cc_final: 0.8547 (p-80) REVERT: B 269 MET cc_start: 0.7175 (mmm) cc_final: 0.6805 (mmt) REVERT: B 294 TYR cc_start: 0.8616 (m-10) cc_final: 0.8340 (m-10) REVERT: C 47 MET cc_start: 0.6590 (tpp) cc_final: 0.6389 (tpp) REVERT: C 78 ASN cc_start: 0.8241 (t0) cc_final: 0.7403 (t0) REVERT: C 81 ASP cc_start: 0.8602 (m-30) cc_final: 0.8319 (m-30) REVERT: C 269 MET cc_start: 0.7327 (tpt) cc_final: 0.6946 (tpt) REVERT: C 283 MET cc_start: 0.8191 (mmm) cc_final: 0.7652 (mmm) REVERT: C 336 LYS cc_start: 0.7966 (mttt) cc_final: 0.7509 (ttpt) REVERT: D 161 HIS cc_start: 0.8979 (p90) cc_final: 0.8707 (p90) REVERT: D 192 ILE cc_start: 0.8976 (tp) cc_final: 0.8770 (tp) REVERT: D 212 ILE cc_start: 0.8946 (mt) cc_final: 0.8722 (mt) REVERT: D 316 GLU cc_start: 0.6790 (mm-30) cc_final: 0.6572 (mm-30) REVERT: E 68 LYS cc_start: 0.8262 (mmtt) cc_final: 0.7996 (mmmt) REVERT: E 292 ASP cc_start: 0.7887 (m-30) cc_final: 0.7609 (m-30) outliers start: 49 outliers final: 33 residues processed: 284 average time/residue: 0.0939 time to fit residues: 42.1280 Evaluate side-chains 263 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 230 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 334 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 72 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 151 optimal weight: 0.0040 chunk 66 optimal weight: 5.9990 overall best weight: 1.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 252 ASN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.111361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.096332 restraints weight = 24134.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.099334 restraints weight = 12374.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.101339 restraints weight = 7704.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.102719 restraints weight = 5499.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.103643 restraints weight = 4292.883| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15220 Z= 0.168 Angle : 0.675 9.350 20660 Z= 0.330 Chirality : 0.046 0.240 2280 Planarity : 0.005 0.051 2630 Dihedral : 28.239 179.489 2330 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 1.09 % Allowed : 3.55 % Favored : 95.36 % Rotamer: Outliers : 3.96 % Allowed : 13.93 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.20), residues: 1830 helix: 0.91 (0.19), residues: 770 sheet: -0.51 (0.28), residues: 300 loop : 0.22 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 116 TYR 0.016 0.001 TYR C 166 PHE 0.014 0.001 PHE B 223 TRP 0.013 0.002 TRP A 86 HIS 0.007 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (15220) covalent geometry : angle 0.67471 / 0.33 (20660) hydrogen bonds : bond 0.03838 / 2.56 ( 765) hydrogen bonds : angle 4.49765 / 3.16 ( 1920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 236 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8897 (mt) cc_final: 0.8666 (mt) REVERT: A 103 THR cc_start: 0.8901 (m) cc_final: 0.8296 (p) REVERT: A 154 ASP cc_start: 0.8494 (t70) cc_final: 0.8047 (t70) REVERT: A 283 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.8102 (mmt) REVERT: B 78 ASN cc_start: 0.8491 (t0) cc_final: 0.7656 (t0) REVERT: B 136 ILE cc_start: 0.8839 (mp) cc_final: 0.8595 (mt) REVERT: C 78 ASN cc_start: 0.8211 (t0) cc_final: 0.7378 (t0) REVERT: C 81 ASP cc_start: 0.8629 (m-30) cc_final: 0.8288 (m-30) REVERT: C 132 MET cc_start: 0.8138 (ppp) cc_final: 0.7647 (ptt) REVERT: C 269 MET cc_start: 0.7381 (tpt) cc_final: 0.7064 (tpt) REVERT: C 283 MET cc_start: 0.8217 (mmm) cc_final: 0.7748 (mmm) REVERT: C 336 LYS cc_start: 0.8025 (mttt) cc_final: 0.7549 (ttpt) REVERT: D 192 ILE cc_start: 0.9108 (tp) cc_final: 0.8863 (tp) REVERT: D 353 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.7076 (mp10) REVERT: E 68 LYS cc_start: 0.8370 (mmtt) cc_final: 0.8042 (mmmt) REVERT: E 82 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8719 (tpt) REVERT: E 206 ARG cc_start: 0.8271 (ttm-80) cc_final: 0.7823 (ttm-80) REVERT: E 299 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7721 (mtm) outliers start: 62 outliers final: 42 residues processed: 277 average time/residue: 0.0894 time to fit residues: 39.9118 Evaluate side-chains 271 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 225 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 299 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 184 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 132 optimal weight: 0.0980 chunk 96 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.098717 restraints weight = 23662.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.101803 restraints weight = 12022.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.103881 restraints weight = 7460.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.105274 restraints weight = 5281.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.106181 restraints weight = 4111.963| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15220 Z= 0.131 Angle : 0.652 8.998 20660 Z= 0.315 Chirality : 0.045 0.190 2280 Planarity : 0.005 0.050 2630 Dihedral : 27.840 178.014 2330 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 1.04 % Allowed : 3.50 % Favored : 95.46 % Rotamer: Outliers : 3.51 % Allowed : 14.70 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.20), residues: 1830 helix: 1.21 (0.20), residues: 735 sheet: -0.51 (0.29), residues: 300 loop : 0.24 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 206 TYR 0.014 0.001 TYR C 166 PHE 0.018 0.001 PHE A 223 TRP 0.013 0.001 TRP A 86 HIS 0.005 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (15220) covalent geometry : angle 0.65198 / 0.32 (20660) hydrogen bonds : bond 0.03338 / 2.19 ( 765) hydrogen bonds : angle 4.40488 / 3.10 ( 1920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 237 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8864 (mt) cc_final: 0.8624 (mt) REVERT: A 103 THR cc_start: 0.8864 (m) cc_final: 0.8305 (p) REVERT: A 154 ASP cc_start: 0.8485 (t70) cc_final: 0.8034 (t70) REVERT: B 136 ILE cc_start: 0.8889 (mp) cc_final: 0.8677 (mt) REVERT: C 40 HIS cc_start: 0.8193 (OUTLIER) cc_final: 0.7716 (m-70) REVERT: C 78 ASN cc_start: 0.8206 (t0) cc_final: 0.7267 (t0) REVERT: C 81 ASP cc_start: 0.8623 (m-30) cc_final: 0.8310 (m-30) REVERT: C 132 MET cc_start: 0.8235 (ppp) cc_final: 0.7562 (ptt) REVERT: C 195 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7842 (mt-10) REVERT: C 269 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.7035 (tpt) REVERT: C 283 MET cc_start: 0.8205 (mmm) cc_final: 0.7770 (mmm) REVERT: C 336 LYS cc_start: 0.8057 (mttt) cc_final: 0.7575 (ttpt) REVERT: D 72 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7320 (pt0) REVERT: D 192 ILE cc_start: 0.9075 (tp) cc_final: 0.8820 (tp) REVERT: D 353 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.7093 (mp10) REVERT: E 47 MET cc_start: 0.3900 (mtt) cc_final: 0.3392 (mtt) REVERT: E 68 LYS cc_start: 0.8352 (mmtt) cc_final: 0.8022 (mmmt) REVERT: E 192 ILE cc_start: 0.9178 (mm) cc_final: 0.8901 (tt) REVERT: E 206 ARG cc_start: 0.8207 (ttm-80) cc_final: 0.7803 (ttm-80) REVERT: E 246 GLN cc_start: 0.8785 (mt0) cc_final: 0.8396 (mt0) REVERT: E 299 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8091 (mtm) REVERT: E 325 MET cc_start: 0.8056 (mmp) cc_final: 0.7334 (mmm) outliers start: 55 outliers final: 41 residues processed: 268 average time/residue: 0.0924 time to fit residues: 39.8001 Evaluate side-chains 269 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 224 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain E residue 334 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 117 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 111 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 GLN C 41 GLN C 115 ASN C 360 GLN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.112741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.097369 restraints weight = 23747.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.100389 restraints weight = 12224.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.102419 restraints weight = 7673.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.103778 restraints weight = 5496.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.104736 restraints weight = 4321.186| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15220 Z= 0.140 Angle : 0.660 10.609 20660 Z= 0.318 Chirality : 0.045 0.196 2280 Planarity : 0.005 0.047 2630 Dihedral : 27.410 178.549 2330 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.98 % Allowed : 3.77 % Favored : 95.25 % Rotamer: Outliers : 3.77 % Allowed : 14.95 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.20), residues: 1830 helix: 1.26 (0.20), residues: 735 sheet: -0.47 (0.29), residues: 300 loop : 0.26 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 206 TYR 0.036 0.001 TYR A 166 PHE 0.017 0.001 PHE A 223 TRP 0.010 0.001 TRP B 86 HIS 0.005 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (15220) covalent geometry : angle 0.66010 / 0.32 (20660) hydrogen bonds : bond 0.03401 / 2.25 ( 765) hydrogen bonds : angle 4.40033 / 3.10 ( 1920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 230 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 ASP cc_start: 0.8499 (t70) cc_final: 0.8050 (t70) REVERT: B 136 ILE cc_start: 0.8990 (mp) cc_final: 0.8775 (mt) REVERT: C 40 HIS cc_start: 0.8235 (OUTLIER) cc_final: 0.7804 (m-70) REVERT: C 47 MET cc_start: 0.7582 (tpp) cc_final: 0.6642 (mtp) REVERT: C 78 ASN cc_start: 0.8239 (t0) cc_final: 0.7278 (t0) REVERT: C 81 ASP cc_start: 0.8642 (m-30) cc_final: 0.8303 (m-30) REVERT: C 132 MET cc_start: 0.8277 (ppp) cc_final: 0.7603 (ptt) REVERT: C 269 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.7030 (tpt) REVERT: C 283 MET cc_start: 0.8263 (mmm) cc_final: 0.7816 (mmm) REVERT: C 336 LYS cc_start: 0.8203 (mttt) cc_final: 0.7690 (ttpt) REVERT: D 72 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7319 (pt0) REVERT: D 192 ILE cc_start: 0.9112 (tp) cc_final: 0.8851 (tp) REVERT: D 353 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7133 (mp10) REVERT: E 47 MET cc_start: 0.4132 (mtt) cc_final: 0.3706 (mtt) REVERT: E 68 LYS cc_start: 0.8344 (mmtt) cc_final: 0.8070 (mmmt) REVERT: E 246 GLN cc_start: 0.8766 (mt0) cc_final: 0.8435 (mt0) REVERT: E 299 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.8045 (mtm) outliers start: 59 outliers final: 48 residues processed: 268 average time/residue: 0.0935 time to fit residues: 40.0470 Evaluate side-chains 269 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 217 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain E residue 334 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 86 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 149 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 chunk 110 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN C 360 GLN D 115 ASN E 12 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.115363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.100220 restraints weight = 23817.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.103248 restraints weight = 12240.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.105285 restraints weight = 7669.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.106582 restraints weight = 5485.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.107581 restraints weight = 4347.364| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15220 Z= 0.117 Angle : 0.649 8.920 20660 Z= 0.313 Chirality : 0.044 0.176 2280 Planarity : 0.005 0.046 2630 Dihedral : 27.095 178.013 2330 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.93 % Allowed : 3.44 % Favored : 95.63 % Rotamer: Outliers : 3.19 % Allowed : 15.78 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.20), residues: 1830 helix: 1.36 (0.20), residues: 735 sheet: -0.40 (0.30), residues: 300 loop : 0.29 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 206 TYR 0.030 0.001 TYR A 166 PHE 0.016 0.001 PHE A 223 TRP 0.013 0.001 TRP B 86 HIS 0.004 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (15220) covalent geometry : angle 0.64919 / 0.31 (20660) hydrogen bonds : bond 0.03076 / 2.02 ( 765) hydrogen bonds : angle 4.32637 / 3.04 ( 1920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 230 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 THR cc_start: 0.8831 (m) cc_final: 0.8468 (p) REVERT: A 154 ASP cc_start: 0.8430 (t70) cc_final: 0.8005 (t70) REVERT: A 285 CYS cc_start: 0.8369 (m) cc_final: 0.8094 (m) REVERT: B 132 MET cc_start: 0.7993 (ptm) cc_final: 0.7691 (ttm) REVERT: B 136 ILE cc_start: 0.8978 (mp) cc_final: 0.8775 (mt) REVERT: C 40 HIS cc_start: 0.8150 (OUTLIER) cc_final: 0.7706 (m-70) REVERT: C 47 MET cc_start: 0.7678 (tpp) cc_final: 0.6704 (mtp) REVERT: C 78 ASN cc_start: 0.8234 (t0) cc_final: 0.7273 (t0) REVERT: C 81 ASP cc_start: 0.8591 (m-30) cc_final: 0.8265 (m-30) REVERT: C 132 MET cc_start: 0.8242 (ppp) cc_final: 0.7624 (ptt) REVERT: C 217 CYS cc_start: 0.8665 (m) cc_final: 0.7872 (m) REVERT: C 269 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.7034 (tpt) REVERT: C 283 MET cc_start: 0.8179 (mmm) cc_final: 0.7702 (mmt) REVERT: C 313 MET cc_start: 0.8227 (tpp) cc_final: 0.7758 (ttp) REVERT: C 336 LYS cc_start: 0.8227 (mttt) cc_final: 0.7648 (ttpt) REVERT: C 337 TYR cc_start: 0.8694 (m-80) cc_final: 0.8045 (m-80) REVERT: D 72 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7314 (pt0) REVERT: D 128 ASN cc_start: 0.8065 (m-40) cc_final: 0.7812 (p0) REVERT: D 192 ILE cc_start: 0.9104 (tp) cc_final: 0.8837 (tp) REVERT: D 353 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7173 (mp10) REVERT: E 68 LYS cc_start: 0.8322 (mmtt) cc_final: 0.8056 (mmmt) REVERT: E 123 MET cc_start: 0.7013 (mmt) cc_final: 0.6811 (mmt) REVERT: E 246 GLN cc_start: 0.8699 (mt0) cc_final: 0.8286 (mt0) outliers start: 50 outliers final: 41 residues processed: 261 average time/residue: 0.0874 time to fit residues: 36.8402 Evaluate side-chains 266 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 222 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 334 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 30 optimal weight: 0.2980 chunk 127 optimal weight: 0.6980 chunk 149 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 23 optimal weight: 0.0270 chunk 17 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 overall best weight: 0.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 12 ASN C 41 GLN C 360 GLN D 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.115504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.100131 restraints weight = 23892.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.103202 restraints weight = 12181.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.105274 restraints weight = 7589.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.106608 restraints weight = 5400.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.107558 restraints weight = 4252.064| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15220 Z= 0.117 Angle : 0.653 8.813 20660 Z= 0.315 Chirality : 0.044 0.172 2280 Planarity : 0.005 0.046 2630 Dihedral : 26.906 179.323 2330 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.87 % Allowed : 3.22 % Favored : 95.90 % Rotamer: Outliers : 3.32 % Allowed : 16.17 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.20), residues: 1830 helix: 1.40 (0.20), residues: 735 sheet: 0.03 (0.30), residues: 330 loop : 0.25 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 206 TYR 0.032 0.001 TYR A 166 PHE 0.020 0.001 PHE A 223 TRP 0.014 0.001 TRP A 79 HIS 0.005 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (15220) covalent geometry : angle 0.65301 / 0.31 (20660) hydrogen bonds : bond 0.03045 / 2.01 ( 765) hydrogen bonds : angle 4.29984 / 3.03 ( 1920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 237 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 103 THR cc_start: 0.8805 (m) cc_final: 0.8412 (p) REVERT: A 223 PHE cc_start: 0.6537 (p90) cc_final: 0.6257 (p90) REVERT: A 285 CYS cc_start: 0.8415 (m) cc_final: 0.8155 (m) REVERT: B 132 MET cc_start: 0.7998 (ptm) cc_final: 0.7705 (ttm) REVERT: B 136 ILE cc_start: 0.8993 (mp) cc_final: 0.8764 (mt) REVERT: C 40 HIS cc_start: 0.8059 (OUTLIER) cc_final: 0.7650 (m-70) REVERT: C 78 ASN cc_start: 0.8242 (t0) cc_final: 0.7282 (t0) REVERT: C 81 ASP cc_start: 0.8573 (m-30) cc_final: 0.8274 (m-30) REVERT: C 132 MET cc_start: 0.8201 (ppp) cc_final: 0.7573 (ptt) REVERT: C 217 CYS cc_start: 0.8653 (m) cc_final: 0.7839 (m) REVERT: C 269 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.7016 (tpt) REVERT: C 283 MET cc_start: 0.8043 (mmm) cc_final: 0.7615 (mmt) REVERT: C 336 LYS cc_start: 0.8226 (mttt) cc_final: 0.7624 (ttpt) REVERT: C 337 TYR cc_start: 0.8687 (m-80) cc_final: 0.8068 (m-80) REVERT: D 72 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7316 (pt0) REVERT: D 128 ASN cc_start: 0.8159 (m-40) cc_final: 0.7873 (p0) REVERT: D 192 ILE cc_start: 0.9073 (tp) cc_final: 0.8798 (tp) REVERT: D 353 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.7168 (mp10) REVERT: E 246 GLN cc_start: 0.8667 (mt0) cc_final: 0.8230 (mt0) outliers start: 52 outliers final: 42 residues processed: 269 average time/residue: 0.0951 time to fit residues: 40.8031 Evaluate side-chains 270 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 225 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 334 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 165 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 HIS B 41 GLN C 360 GLN D 296 ASN E 252 ASN E 353 GLN E 354 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.112597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.097153 restraints weight = 23934.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.100152 restraints weight = 12326.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.102170 restraints weight = 7752.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.103455 restraints weight = 5582.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.104400 restraints weight = 4441.060| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.5884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15220 Z= 0.169 Angle : 0.700 10.389 20660 Z= 0.336 Chirality : 0.046 0.180 2280 Planarity : 0.005 0.047 2630 Dihedral : 26.841 179.527 2330 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.82 % Allowed : 4.10 % Favored : 95.08 % Rotamer: Outliers : 3.51 % Allowed : 16.49 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.20), residues: 1830 helix: 1.26 (0.20), residues: 735 sheet: -0.32 (0.31), residues: 300 loop : 0.23 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 206 TYR 0.034 0.001 TYR A 166 PHE 0.021 0.001 PHE A 223 TRP 0.023 0.002 TRP A 86 HIS 0.006 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (15220) covalent geometry : angle 0.69954 / 0.34 (20660) hydrogen bonds : bond 0.03539 / 2.34 ( 765) hydrogen bonds : angle 4.40106 / 3.10 ( 1920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 225 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 THR cc_start: 0.8789 (m) cc_final: 0.8462 (p) REVERT: A 154 ASP cc_start: 0.8472 (t70) cc_final: 0.8068 (t70) REVERT: A 223 PHE cc_start: 0.6767 (p90) cc_final: 0.6510 (p90) REVERT: A 285 CYS cc_start: 0.8513 (m) cc_final: 0.8269 (m) REVERT: B 136 ILE cc_start: 0.8976 (mp) cc_final: 0.8763 (mt) REVERT: B 269 MET cc_start: 0.7271 (mtt) cc_final: 0.6993 (mtt) REVERT: C 40 HIS cc_start: 0.8192 (OUTLIER) cc_final: 0.7778 (m-70) REVERT: C 47 MET cc_start: 0.7802 (tpp) cc_final: 0.6698 (mtp) REVERT: C 78 ASN cc_start: 0.8276 (t0) cc_final: 0.8029 (t0) REVERT: C 132 MET cc_start: 0.8310 (ppp) cc_final: 0.7663 (ptt) REVERT: C 269 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.7051 (tpt) REVERT: C 283 MET cc_start: 0.8180 (mmm) cc_final: 0.7676 (mmt) REVERT: C 313 MET cc_start: 0.8268 (tpp) cc_final: 0.7780 (ttp) REVERT: C 336 LYS cc_start: 0.8291 (mttt) cc_final: 0.7711 (ttpt) REVERT: D 72 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7321 (pt0) REVERT: D 128 ASN cc_start: 0.8220 (m-40) cc_final: 0.7967 (p0) REVERT: D 192 ILE cc_start: 0.9102 (tp) cc_final: 0.8859 (tp) REVERT: D 353 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7230 (mp10) REVERT: D 355 MET cc_start: 0.8192 (mtp) cc_final: 0.7925 (mtp) REVERT: E 82 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8778 (tpt) REVERT: E 206 ARG cc_start: 0.8175 (ttm-80) cc_final: 0.7908 (ttm-80) REVERT: E 246 GLN cc_start: 0.8771 (mt0) cc_final: 0.8320 (mt0) REVERT: E 353 GLN cc_start: 0.7640 (mp-120) cc_final: 0.7209 (mp10) outliers start: 55 outliers final: 45 residues processed: 260 average time/residue: 0.0945 time to fit residues: 39.3654 Evaluate side-chains 268 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 219 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 334 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 140 optimal weight: 0.6980 chunk 177 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN E 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.114133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.098579 restraints weight = 23742.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.101631 restraints weight = 12255.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.103683 restraints weight = 7674.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.105057 restraints weight = 5507.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.105992 restraints weight = 4335.140| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.5950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15220 Z= 0.131 Angle : 0.676 9.833 20660 Z= 0.324 Chirality : 0.045 0.172 2280 Planarity : 0.005 0.044 2630 Dihedral : 26.673 179.556 2330 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.82 % Allowed : 3.77 % Favored : 95.41 % Rotamer: Outliers : 3.32 % Allowed : 16.87 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.20), residues: 1830 helix: 1.35 (0.20), residues: 735 sheet: -0.05 (0.30), residues: 335 loop : 0.26 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 206 TYR 0.031 0.001 TYR A 166 PHE 0.020 0.001 PHE A 223 TRP 0.021 0.002 TRP A 86 HIS 0.005 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (15220) covalent geometry : angle 0.67578 / 0.32 (20660) hydrogen bonds : bond 0.03187 / 2.11 ( 765) hydrogen bonds : angle 4.33454 / 3.05 ( 1920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2211.79 seconds wall clock time: 39 minutes 15.21 seconds (2355.21 seconds total)